src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.GeneticCodeI;
  28 import jalview.analysis.ParseProperties;
  29 import jalview.analysis.SequenceIdMatcher;
  30 import jalview.api.AlignExportSettingI;
  31 import jalview.api.AlignViewControllerGuiI;
  32 import jalview.api.AlignViewControllerI;
  33 import jalview.api.AlignViewportI;
  34 import jalview.api.AlignmentViewPanel;
  35 import jalview.api.FeatureSettingsControllerI;
  36 import jalview.api.SplitContainerI;
  37 import jalview.api.ViewStyleI;
  38 import jalview.api.analysis.SimilarityParamsI;
  39 import jalview.bin.Cache;
  40 import jalview.bin.Jalview;
  41 import jalview.commands.CommandI;
  42 import jalview.commands.EditCommand;
  43 import jalview.commands.EditCommand.Action;
  44 import jalview.commands.OrderCommand;
  45 import jalview.commands.RemoveGapColCommand;
  46 import jalview.commands.RemoveGapsCommand;
  47 import jalview.commands.SlideSequencesCommand;
  48 import jalview.commands.TrimRegionCommand;
  49 import jalview.datamodel.AlignedCodonFrame;
  50 import jalview.datamodel.Alignment;
  51 import jalview.datamodel.AlignmentAnnotation;
  52 import jalview.datamodel.AlignmentExportData;
  53 import jalview.datamodel.AlignmentI;
  54 import jalview.datamodel.AlignmentOrder;
  55 import jalview.datamodel.AlignmentView;
  56 import jalview.datamodel.ColumnSelection;
  57 import jalview.datamodel.HiddenColumns;
  58 import jalview.datamodel.HiddenSequences;
  59 import jalview.datamodel.PDBEntry;
  60 import jalview.datamodel.SeqCigar;
  61 import jalview.datamodel.Sequence;
  62 import jalview.datamodel.SequenceGroup;
  63 import jalview.datamodel.SequenceI;
  64 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  65 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  66 import jalview.io.AlignmentProperties;
  67 import jalview.io.AnnotationFile;
  68 import jalview.io.BioJsHTMLOutput;
  69 import jalview.io.DataSourceType;
  70 import jalview.io.FileFormat;
  71 import jalview.io.FileFormatI;
  72 import jalview.io.FileFormats;
  73 import jalview.io.FileLoader;
  74 import jalview.io.FileParse;
  75 import jalview.io.FormatAdapter;
  76 import jalview.io.HtmlSvgOutput;
  77 import jalview.io.IdentifyFile;
  78 import jalview.io.JPredFile;
  79 import jalview.io.JalviewFileChooser;
  80 import jalview.io.JalviewFileView;
  81 import jalview.io.JnetAnnotationMaker;
  82 import jalview.io.NewickFile;
  83 import jalview.io.ScoreMatrixFile;
  84 import jalview.io.TCoffeeScoreFile;
  85 import jalview.io.vcf.VCFLoader;
  86 import jalview.jbgui.GAlignFrame;
  87 import jalview.schemes.ColourSchemeI;
  88 import jalview.schemes.ColourSchemes;
  89 import jalview.schemes.ResidueColourScheme;
  90 import jalview.schemes.TCoffeeColourScheme;
  91 import jalview.util.MessageManager;
  92 import jalview.viewmodel.AlignmentViewport;
  93 import jalview.viewmodel.ViewportRanges;
  94 import jalview.ws.DBRefFetcher;
  95 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  96 import jalview.ws.jws1.Discoverer;
  97 import jalview.ws.jws2.Jws2Discoverer;
  98 import jalview.ws.jws2.jabaws2.Jws2Instance;
  99 import jalview.ws.seqfetcher.DbSourceProxy;
 100
 101 import java.awt.BorderLayout;
 102 import java.awt.Component;
 103 import java.awt.Rectangle;
 104 import java.awt.Toolkit;
 105 import java.awt.datatransfer.Clipboard;
 106 import java.awt.datatransfer.DataFlavor;
 107 import java.awt.datatransfer.StringSelection;
 108 import java.awt.datatransfer.Transferable;
 109 import java.awt.dnd.DnDConstants;
 110 import java.awt.dnd.DropTargetDragEvent;
 111 import java.awt.dnd.DropTargetDropEvent;
 112 import java.awt.dnd.DropTargetEvent;
 113 import java.awt.dnd.DropTargetListener;
 114 import java.awt.event.ActionEvent;
 115 import java.awt.event.ActionListener;
 116 import java.awt.event.FocusAdapter;
 117 import java.awt.event.FocusEvent;
 118 import java.awt.event.ItemEvent;
 119 import java.awt.event.ItemListener;
 120 import java.awt.event.KeyAdapter;
 121 import java.awt.event.KeyEvent;
 122 import java.awt.event.MouseEvent;
 123 import java.awt.print.PageFormat;
 124 import java.awt.print.PrinterJob;
 125 import java.beans.PropertyChangeEvent;
 126 import java.io.File;
 127 import java.io.FileWriter;
 128 import java.io.PrintWriter;
 129 import java.net.URL;
 130 import java.util.ArrayList;
 131 import java.util.Arrays;
 132 import java.util.Deque;
 133 import java.util.Enumeration;
 134 import java.util.Hashtable;
 135 import java.util.List;
 136 import java.util.Vector;
 137
 138 import javax.swing.JCheckBoxMenuItem;
 139 import javax.swing.JEditorPane;
 140 import javax.swing.JInternalFrame;
 141 import javax.swing.JLayeredPane;
 142 import javax.swing.JMenu;
 143 import javax.swing.JMenuItem;
 144 import javax.swing.JScrollPane;
 145 import javax.swing.SwingUtilities;
 146
 147 /**
 148  * DOCUMENT ME!
 149  *
 150  * @author $author$
 151  * @version $Revision$
 152  */
 153 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 154         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 155 {
 156
 157   public static final int DEFAULT_WIDTH = 700;
 158
 159   public static final int DEFAULT_HEIGHT = 500;
 160
 161   /*
 162    * The currently displayed panel (selected tabbed view if more than one)
 163    */
 164   public AlignmentPanel alignPanel;
 165
 166   AlignViewport viewport;
 167
 168   public AlignViewControllerI avc;
 169
 170   List<AlignmentPanel> alignPanels = new ArrayList<>();
 171
 172   /**
 173    * Last format used to load or save alignments in this window
 174    */
 175   FileFormatI currentFileFormat = null;
 176
 177   /**
 178    * Current filename for this alignment
 179    */
 180   String fileName = null;
 181
 182   /**
 183    * Creates a new AlignFrame object with specific width and height.
 184    *
 185    * @param al
 186    * @param width
 187    * @param height
 188    */
 189   public AlignFrame(AlignmentI al, int width, int height)
 190   {
 191     this(al, null, width, height);
 192   }
 193
 194   /**
 195    * Creates a new AlignFrame object with specific width, height and
 196    * sequenceSetId
 197    *
 198    * @param al
 199    * @param width
 200    * @param height
 201    * @param sequenceSetId
 202    */
 203   public AlignFrame(AlignmentI al, int width, int height,
 204           String sequenceSetId)
 205   {
 206     this(al, null, width, height, sequenceSetId);
 207   }
 208
 209   /**
 210    * Creates a new AlignFrame object with specific width, height and
 211    * sequenceSetId
 212    *
 213    * @param al
 214    * @param width
 215    * @param height
 216    * @param sequenceSetId
 217    * @param viewId
 218    */
 219   public AlignFrame(AlignmentI al, int width, int height,
 220           String sequenceSetId, String viewId)
 221   {
 222     this(al, null, width, height, sequenceSetId, viewId);
 223   }
 224
 225   /**
 226    * new alignment window with hidden columns
 227    *
 228    * @param al
 229    *          AlignmentI
 230    * @param hiddenColumns
 231    *          ColumnSelection or null
 232    * @param width
 233    *          Width of alignment frame
 234    * @param height
 235    *          height of frame.
 236    */
 237   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 238           int height)
 239   {
 240     this(al, hiddenColumns, width, height, null);
 241   }
 242
 243   /**
 244    * Create alignment frame for al with hiddenColumns, a specific width and
 245    * height, and specific sequenceId
 246    *
 247    * @param al
 248    * @param hiddenColumns
 249    * @param width
 250    * @param height
 251    * @param sequenceSetId
 252    *          (may be null)
 253    */
 254   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 255           int height, String sequenceSetId)
 256   {
 257     this(al, hiddenColumns, width, height, sequenceSetId, null);
 258   }
 259
 260   /**
 261    * Create alignment frame for al with hiddenColumns, a specific width and
 262    * height, and specific sequenceId
 263    *
 264    * @param al
 265    * @param hiddenColumns
 266    * @param width
 267    * @param height
 268    * @param sequenceSetId
 269    *          (may be null)
 270    * @param viewId
 271    *          (may be null)
 272    */
 273   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 274           int height, String sequenceSetId, String viewId)
 275   {
 276     setSize(width, height);
 277
 278     if (al.getDataset() == null)
 279     {
 280       al.setDataset(null);
 281     }
 282
 283     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 284
 285     alignPanel = new AlignmentPanel(this, viewport);
 286
 287     addAlignmentPanel(alignPanel, true);
 288     init();
 289   }
 290
 291   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 292           HiddenColumns hiddenColumns, int width, int height)
 293   {
 294     setSize(width, height);
 295
 296     if (al.getDataset() == null)
 297     {
 298       al.setDataset(null);
 299     }
 300
 301     viewport = new AlignViewport(al, hiddenColumns);
 302
 303     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 304     {
 305       viewport.hideSequence(hiddenSeqs);
 306     }
 307     alignPanel = new AlignmentPanel(this, viewport);
 308     addAlignmentPanel(alignPanel, true);
 309     init();
 310   }
 311
 312   /**
 313    * Make a new AlignFrame from existing alignmentPanels
 314    *
 315    * @param ap
 316    *          AlignmentPanel
 317    * @param av
 318    *          AlignViewport
 319    */
 320   public AlignFrame(AlignmentPanel ap)
 321   {
 322     viewport = ap.av;
 323     alignPanel = ap;
 324     addAlignmentPanel(ap, false);
 325     init();
 326   }
 327
 328   /**
 329    * initalise the alignframe from the underlying viewport data and the
 330    * configurations
 331    */
 332   void init()
 333   {
 334     if (!Jalview.isHeadlessMode())
 335     {
 336       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 337     }
 338
 339     avc = new jalview.controller.AlignViewController(this, viewport,
 340             alignPanel);
 341     if (viewport.getAlignmentConservationAnnotation() == null)
 342     {
 343       // BLOSUM62Colour.setEnabled(false);
 344       conservationMenuItem.setEnabled(false);
 345       modifyConservation.setEnabled(false);
 346       // PIDColour.setEnabled(false);
 347       // abovePIDThreshold.setEnabled(false);
 348       // modifyPID.setEnabled(false);
 349     }
 350
 351     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 352             "No sort");
 353
 354     if (sortby.equals("Id"))
 355     {
 356       sortIDMenuItem_actionPerformed(null);
 357     }
 358     else if (sortby.equals("Pairwise Identity"))
 359     {
 360       sortPairwiseMenuItem_actionPerformed(null);
 361     }
 362
 363     this.alignPanel.av
 364             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 365
 366     setMenusFromViewport(viewport);
 367     buildSortByAnnotationScoresMenu();
 368     calculateTree.addActionListener(new ActionListener()
 369     {
 370
 371       @Override
 372       public void actionPerformed(ActionEvent e)
 373       {
 374         openTreePcaDialog();
 375       }
 376     });
 377     buildColourMenu();
 378
 379     if (Desktop.desktop != null)
 380     {
 381       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 382       addServiceListeners();
 383       setGUINucleotide();
 384     }
 385
 386     if (viewport.getWrapAlignment())
 387     {
 388       wrapMenuItem_actionPerformed(null);
 389     }
 390
 391     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 392     {
 393       this.overviewMenuItem_actionPerformed(null);
 394     }
 395
 396     addKeyListener();
 397
 398     final List<AlignmentPanel> selviews = new ArrayList<>();
 399     final List<AlignmentPanel> origview = new ArrayList<>();
 400     final String menuLabel = MessageManager
 401             .getString("label.copy_format_from");
 402     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 403             new ViewSetProvider()
 404             {
 405
 406               @Override
 407               public AlignmentPanel[] getAllAlignmentPanels()
 408               {
 409                 origview.clear();
 410                 origview.add(alignPanel);
 411                 // make an array of all alignment panels except for this one
 412                 List<AlignmentPanel> aps = new ArrayList<>(
 413                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 414                 aps.remove(AlignFrame.this.alignPanel);
 415                 return aps.toArray(new AlignmentPanel[aps.size()]);
 416               }
 417             }, selviews, new ItemListener()
 418             {
 419
 420               @Override
 421               public void itemStateChanged(ItemEvent e)
 422               {
 423                 if (origview.size() > 0)
 424                 {
 425                   final AlignmentPanel ap = origview.get(0);
 426
 427                   /*
 428                    * Copy the ViewStyle of the selected panel to 'this one'.
 429                    * Don't change value of 'scaleProteinAsCdna' unless copying
 430                    * from a SplitFrame.
 431                    */
 432                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 433                           .getViewStyle();
 434                   boolean fromSplitFrame = selviews.get(0)
 435                           .getAlignViewport().getCodingComplement() != null;
 436                   if (!fromSplitFrame)
 437                   {
 438                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 439                             .getViewStyle().isScaleProteinAsCdna());
 440                   }
 441                   ap.getAlignViewport().setViewStyle(vs);
 442
 443                   /*
 444                    * Also rescale ViewStyle of SplitFrame complement if there is
 445                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 446                    * the whole ViewStyle (allow cDNA protein to have different
 447                    * fonts)
 448                    */
 449                   AlignViewportI complement = ap.getAlignViewport()
 450                           .getCodingComplement();
 451                   if (complement != null && vs.isScaleProteinAsCdna())
 452                   {
 453                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 454                     ((SplitFrame) af.getSplitViewContainer())
 455                             .adjustLayout();
 456                     af.setMenusForViewport();
 457                   }
 458
 459                   ap.updateLayout();
 460                   ap.setSelected(true);
 461                   ap.alignFrame.setMenusForViewport();
 462
 463                 }
 464               }
 465             });
 466     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 467             .indexOf("devel") > -1
 468             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 469                     .indexOf("test") > -1)
 470     {
 471       formatMenu.add(vsel);
 472     }
 473     addFocusListener(new FocusAdapter()
 474     {
 475       @Override
 476       public void focusGained(FocusEvent e)
 477       {
 478         Jalview.setCurrentAlignFrame(AlignFrame.this);
 479       }
 480     });
 481
 482   }
 483
 484   /**
 485    * Change the filename and format for the alignment, and enable the 'reload'
 486    * button functionality.
 487    *
 488    * @param file
 489    *          valid filename
 490    * @param format
 491    *          format of file
 492    */
 493   public void setFileName(String file, FileFormatI format)
 494   {
 495     fileName = file;
 496     setFileFormat(format);
 497     reload.setEnabled(true);
 498   }
 499
 500   /**
 501    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 502    * events
 503    */
 504   void addKeyListener()
 505   {
 506     addKeyListener(new KeyAdapter()
 507     {
 508       @Override
 509       public void keyPressed(KeyEvent evt)
 510       {
 511         if (viewport.cursorMode
 512                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 513                         && evt.getKeyCode() <= KeyEvent.VK_9)
 514                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 515                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 516                 && Character.isDigit(evt.getKeyChar()))
 517         {
 518           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 519         }
 520
 521         switch (evt.getKeyCode())
 522         {
 523
 524         case 27: // escape key
 525           deselectAllSequenceMenuItem_actionPerformed(null);
 526
 527           break;
 528
 529         case KeyEvent.VK_DOWN:
 530           if (evt.isAltDown() || !viewport.cursorMode)
 531           {
 532             moveSelectedSequences(false);
 533           }
 534           if (viewport.cursorMode)
 535           {
 536             alignPanel.getSeqPanel().moveCursor(0, 1);
 537           }
 538           break;
 539
 540         case KeyEvent.VK_UP:
 541           if (evt.isAltDown() || !viewport.cursorMode)
 542           {
 543             moveSelectedSequences(true);
 544           }
 545           if (viewport.cursorMode)
 546           {
 547             alignPanel.getSeqPanel().moveCursor(0, -1);
 548           }
 549
 550           break;
 551
 552         case KeyEvent.VK_LEFT:
 553           if (evt.isAltDown() || !viewport.cursorMode)
 554           {
 555             slideSequences(false,
 556                     alignPanel.getSeqPanel().getKeyboardNo1());
 557           }
 558           else
 559           {
 560             alignPanel.getSeqPanel().moveCursor(-1, 0);
 561           }
 562
 563           break;
 564
 565         case KeyEvent.VK_RIGHT:
 566           if (evt.isAltDown() || !viewport.cursorMode)
 567           {
 568             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 569           }
 570           else
 571           {
 572             alignPanel.getSeqPanel().moveCursor(1, 0);
 573           }
 574           break;
 575
 576         case KeyEvent.VK_SPACE:
 577           if (viewport.cursorMode)
 578           {
 579             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 580                     || evt.isShiftDown() || evt.isAltDown());
 581           }
 582           break;
 583
 584         // case KeyEvent.VK_A:
 585         // if (viewport.cursorMode)
 586         // {
 587         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 588         // //System.out.println("A");
 589         // }
 590         // break;
 591         /*
 592          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 593          * System.out.println("closing bracket"); } break;
 594          */
 595         case KeyEvent.VK_DELETE:
 596         case KeyEvent.VK_BACK_SPACE:
 597           if (!viewport.cursorMode)
 598           {
 599             cut_actionPerformed(null);
 600           }
 601           else
 602           {
 603             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 604                     || evt.isShiftDown() || evt.isAltDown());
 605           }
 606
 607           break;
 608
 609         case KeyEvent.VK_S:
 610           if (viewport.cursorMode)
 611           {
 612             alignPanel.getSeqPanel().setCursorRow();
 613           }
 614           break;
 615         case KeyEvent.VK_C:
 616           if (viewport.cursorMode && !evt.isControlDown())
 617           {
 618             alignPanel.getSeqPanel().setCursorColumn();
 619           }
 620           break;
 621         case KeyEvent.VK_P:
 622           if (viewport.cursorMode)
 623           {
 624             alignPanel.getSeqPanel().setCursorPosition();
 625           }
 626           break;
 627
 628         case KeyEvent.VK_ENTER:
 629         case KeyEvent.VK_COMMA:
 630           if (viewport.cursorMode)
 631           {
 632             alignPanel.getSeqPanel().setCursorRowAndColumn();
 633           }
 634           break;
 635
 636         case KeyEvent.VK_Q:
 637           if (viewport.cursorMode)
 638           {
 639             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 640           }
 641           break;
 642         case KeyEvent.VK_M:
 643           if (viewport.cursorMode)
 644           {
 645             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 646           }
 647           break;
 648
 649         case KeyEvent.VK_F2:
 650           viewport.cursorMode = !viewport.cursorMode;
 651           statusBar.setText(MessageManager
 652                   .formatMessage("label.keyboard_editing_mode", new String[]
 653                   { (viewport.cursorMode ? "on" : "off") }));
 654           if (viewport.cursorMode)
 655           {
 656             ViewportRanges ranges = viewport.getRanges();
 657             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 658                     .getStartRes();
 659             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 660                     .getStartSeq();
 661           }
 662           alignPanel.getSeqPanel().seqCanvas.repaint();
 663           break;
 664
 665         case KeyEvent.VK_F1:
 666           try
 667           {
 668             Help.showHelpWindow();
 669           } catch (Exception ex)
 670           {
 671             ex.printStackTrace();
 672           }
 673           break;
 674         case KeyEvent.VK_H:
 675         {
 676           boolean toggleSeqs = !evt.isControlDown();
 677           boolean toggleCols = !evt.isShiftDown();
 678           toggleHiddenRegions(toggleSeqs, toggleCols);
 679           break;
 680         }
 681         case KeyEvent.VK_B:
 682         {
 683           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 684           boolean modifyExisting = true; // always modify, don't clear
 685                                          // evt.isShiftDown();
 686           boolean invertHighlighted = evt.isAltDown();
 687           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 688                   toggleSel);
 689           break;
 690         }
 691         case KeyEvent.VK_PAGE_UP:
 692           viewport.getRanges().pageUp();
 693           break;
 694         case KeyEvent.VK_PAGE_DOWN:
 695           viewport.getRanges().pageDown();
 696           break;
 697         }
 698       }
 699
 700       @Override
 701       public void keyReleased(KeyEvent evt)
 702       {
 703         switch (evt.getKeyCode())
 704         {
 705         case KeyEvent.VK_LEFT:
 706           if (evt.isAltDown() || !viewport.cursorMode)
 707           {
 708             viewport.firePropertyChange("alignment", null,
 709                     viewport.getAlignment().getSequences());
 710           }
 711           break;
 712
 713         case KeyEvent.VK_RIGHT:
 714           if (evt.isAltDown() || !viewport.cursorMode)
 715           {
 716             viewport.firePropertyChange("alignment", null,
 717                     viewport.getAlignment().getSequences());
 718           }
 719           break;
 720         }
 721       }
 722     });
 723   }
 724
 725   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 726   {
 727     ap.alignFrame = this;
 728     avc = new jalview.controller.AlignViewController(this, viewport,
 729             alignPanel);
 730
 731     alignPanels.add(ap);
 732
 733     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 734
 735     int aSize = alignPanels.size();
 736
 737     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 738
 739     if (aSize == 1 && ap.av.viewName == null)
 740     {
 741       this.getContentPane().add(ap, BorderLayout.CENTER);
 742     }
 743     else
 744     {
 745       if (aSize == 2)
 746       {
 747         setInitialTabVisible();
 748       }
 749
 750       expandViews.setEnabled(true);
 751       gatherViews.setEnabled(true);
 752       tabbedPane.addTab(ap.av.viewName, ap);
 753
 754       ap.setVisible(false);
 755     }
 756
 757     if (newPanel)
 758     {
 759       if (ap.av.isPadGaps())
 760       {
 761         ap.av.getAlignment().padGaps();
 762       }
 763       ap.av.updateConservation(ap);
 764       ap.av.updateConsensus(ap);
 765       ap.av.updateStrucConsensus(ap);
 766     }
 767   }
 768
 769   public void setInitialTabVisible()
 770   {
 771     expandViews.setEnabled(true);
 772     gatherViews.setEnabled(true);
 773     tabbedPane.setVisible(true);
 774     AlignmentPanel first = alignPanels.get(0);
 775     tabbedPane.addTab(first.av.viewName, first);
 776     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 777   }
 778
 779   public AlignViewport getViewport()
 780   {
 781     return viewport;
 782   }
 783
 784   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 785   private void addServiceListeners()
 786   {
 787     final java.beans.PropertyChangeListener thisListener;
 788     Desktop.instance.addJalviewPropertyChangeListener("services",
 789             thisListener = new java.beans.PropertyChangeListener()
 790             {
 791               @Override
 792               public void propertyChange(PropertyChangeEvent evt)
 793               {
 794                 // // System.out.println("Discoverer property change.");
 795                 // if (evt.getPropertyName().equals("services"))
 796                 {
 797                   SwingUtilities.invokeLater(new Runnable()
 798                   {
 799
 800                     @Override
 801                     public void run()
 802                     {
 803                       System.err.println(
 804                               "Rebuild WS Menu for service change");
 805                       BuildWebServiceMenu();
 806                     }
 807
 808                   });
 809                 }
 810               }
 811             });
 812     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 813     {
 814       @Override
 815       public void internalFrameClosed(
 816               javax.swing.event.InternalFrameEvent evt)
 817       {
 818         // System.out.println("deregistering discoverer listener");
 819         Desktop.instance.removeJalviewPropertyChangeListener("services",
 820                 thisListener);
 821         closeMenuItem_actionPerformed(true);
 822       };
 823     });
 824     // Finally, build the menu once to get current service state
 825     new Thread(new Runnable()
 826     {
 827       @Override
 828       public void run()
 829       {
 830         BuildWebServiceMenu();
 831       }
 832     }).start();
 833   }
 834
 835   /**
 836    * Configure menu items that vary according to whether the alignment is
 837    * nucleotide or protein
 838    */
 839   public void setGUINucleotide()
 840   {
 841     AlignmentI al = getViewport().getAlignment();
 842     boolean nucleotide = al.isNucleotide();
 843
 844     loadVcf.setVisible(nucleotide);
 845     showTranslation.setVisible(nucleotide);
 846     showReverse.setVisible(nucleotide);
 847     showReverseComplement.setVisible(nucleotide);
 848     conservationMenuItem.setEnabled(!nucleotide);
 849     modifyConservation
 850             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 851     showGroupConservation.setEnabled(!nucleotide);
 852
 853     showComplementMenuItem
 854             .setText(nucleotide ? MessageManager.getString("label.protein")
 855                     : MessageManager.getString("label.nucleotide"));
 856   }
 857
 858   /**
 859    * set up menus for the current viewport. This may be called after any
 860    * operation that affects the data in the current view (selection changed,
 861    * etc) to update the menus to reflect the new state.
 862    */
 863   @Override
 864   public void setMenusForViewport()
 865   {
 866     setMenusFromViewport(viewport);
 867   }
 868
 869   /**
 870    * Need to call this method when tabs are selected for multiple views, or when
 871    * loading from Jalview2XML.java
 872    *
 873    * @param av
 874    *          AlignViewport
 875    */
 876   void setMenusFromViewport(AlignViewport av)
 877   {
 878     padGapsMenuitem.setSelected(av.isPadGaps());
 879     colourTextMenuItem.setSelected(av.isShowColourText());
 880     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 881     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 882     conservationMenuItem.setSelected(av.getConservationSelected());
 883     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 884     seqLimits.setSelected(av.getShowJVSuffix());
 885     idRightAlign.setSelected(av.isRightAlignIds());
 886     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 887     renderGapsMenuItem.setSelected(av.isRenderGaps());
 888     wrapMenuItem.setSelected(av.getWrapAlignment());
 889     scaleAbove.setVisible(av.getWrapAlignment());
 890     scaleLeft.setVisible(av.getWrapAlignment());
 891     scaleRight.setVisible(av.getWrapAlignment());
 892     annotationPanelMenuItem.setState(av.isShowAnnotation());
 893     /*
 894      * Show/hide annotations only enabled if annotation panel is shown
 895      */
 896     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 897     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 898     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 899     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 900     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 901     viewTextMenuItem.setSelected(av.getShowText());
 902     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 903     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 904     showGroupConservation.setSelected(av.isShowGroupConservation());
 905     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 906     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 907     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 908
 909     ColourMenuHelper.setColourSelected(colourMenu,
 910             av.getGlobalColourScheme());
 911
 912     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 913     hiddenMarkers.setState(av.getShowHiddenMarkers());
 914     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 915     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 916     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 917     autoCalculate.setSelected(av.autoCalculateConsensus);
 918     sortByTree.setSelected(av.sortByTree);
 919     listenToViewSelections.setSelected(av.followSelection);
 920
 921     showProducts.setEnabled(canShowProducts());
 922     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 923
 924     updateEditMenuBar();
 925   }
 926
 927   /**
 928    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 929    *
 930    * @param b
 931    */
 932   public void setGroovyEnabled(boolean b)
 933   {
 934     runGroovy.setEnabled(b);
 935   }
 936
 937   private IProgressIndicator progressBar;
 938
 939   /*
 940    * (non-Javadoc)
 941    *
 942    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 943    */
 944   @Override
 945   public void setProgressBar(String message, long id)
 946   {
 947     progressBar.setProgressBar(message, id);
 948   }
 949
 950   @Override
 951   public void registerHandler(final long id,
 952           final IProgressIndicatorHandler handler)
 953   {
 954     progressBar.registerHandler(id, handler);
 955   }
 956
 957   /**
 958    *
 959    * @return true if any progress bars are still active
 960    */
 961   @Override
 962   public boolean operationInProgress()
 963   {
 964     return progressBar.operationInProgress();
 965   }
 966
 967   @Override
 968   public void setStatus(String text)
 969   {
 970     statusBar.setText(text);
 971   }
 972
 973   /*
 974    * Added so Castor Mapping file can obtain Jalview Version
 975    */
 976   public String getVersion()
 977   {
 978     return jalview.bin.Cache.getProperty("VERSION");
 979   }
 980
 981   public FeatureRenderer getFeatureRenderer()
 982   {
 983     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 984   }
 985
 986   @Override
 987   public void fetchSequence_actionPerformed(ActionEvent e)
 988   {
 989     new jalview.gui.SequenceFetcher(this);
 990   }
 991
 992   @Override
 993   public void addFromFile_actionPerformed(ActionEvent e)
 994   {
 995     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 996   }
 997
 998   @Override
 999   public void reload_actionPerformed(ActionEvent e)
1000   {
1001     if (fileName != null)
1002     {
1003       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1004       // originating file's format
1005       // TODO: work out how to recover feature settings for correct view(s) when
1006       // file is reloaded.
1007       if (FileFormat.Jalview.equals(currentFileFormat))
1008       {
1009         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1010         for (int i = 0; i < frames.length; i++)
1011         {
1012           if (frames[i] instanceof AlignFrame && frames[i] != this
1013                   && ((AlignFrame) frames[i]).fileName != null
1014                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1015           {
1016             try
1017             {
1018               frames[i].setSelected(true);
1019               Desktop.instance.closeAssociatedWindows();
1020             } catch (java.beans.PropertyVetoException ex)
1021             {
1022             }
1023           }
1024
1025         }
1026         Desktop.instance.closeAssociatedWindows();
1027
1028         FileLoader loader = new FileLoader();
1029         DataSourceType protocol = fileName.startsWith("http:")
1030                 ? DataSourceType.URL
1031                 : DataSourceType.FILE;
1032         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1033       }
1034       else
1035       {
1036         Rectangle bounds = this.getBounds();
1037
1038         FileLoader loader = new FileLoader();
1039         DataSourceType protocol = fileName.startsWith("http:")
1040                 ? DataSourceType.URL
1041                 : DataSourceType.FILE;
1042         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1043                 protocol, currentFileFormat);
1044
1045         newframe.setBounds(bounds);
1046         if (featureSettings != null && featureSettings.isShowing())
1047         {
1048           final Rectangle fspos = featureSettings.frame.getBounds();
1049           // TODO: need a 'show feature settings' function that takes bounds -
1050           // need to refactor Desktop.addFrame
1051           newframe.featureSettings_actionPerformed(null);
1052           final FeatureSettings nfs = newframe.featureSettings;
1053           SwingUtilities.invokeLater(new Runnable()
1054           {
1055             @Override
1056             public void run()
1057             {
1058               nfs.frame.setBounds(fspos);
1059             }
1060           });
1061           this.featureSettings.close();
1062           this.featureSettings = null;
1063         }
1064         this.closeMenuItem_actionPerformed(true);
1065       }
1066     }
1067   }
1068
1069   @Override
1070   public void addFromText_actionPerformed(ActionEvent e)
1071   {
1072     Desktop.instance
1073             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1074   }
1075
1076   @Override
1077   public void addFromURL_actionPerformed(ActionEvent e)
1078   {
1079     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1080   }
1081
1082   @Override
1083   public void save_actionPerformed(ActionEvent e)
1084   {
1085     if (fileName == null || (currentFileFormat == null)
1086             || fileName.startsWith("http"))
1087     {
1088       saveAs_actionPerformed(null);
1089     }
1090     else
1091     {
1092       saveAlignment(fileName, currentFileFormat);
1093     }
1094   }
1095
1096   /**
1097    * DOCUMENT ME!
1098    *
1099    * @param e
1100    *          DOCUMENT ME!
1101    */
1102   @Override
1103   public void saveAs_actionPerformed(ActionEvent e)
1104   {
1105     String format = currentFileFormat == null ? null
1106             : currentFileFormat.getName();
1107     JalviewFileChooser chooser = JalviewFileChooser
1108             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1109
1110     chooser.setFileView(new JalviewFileView());
1111     chooser.setDialogTitle(
1112             MessageManager.getString("label.save_alignment_to_file"));
1113     chooser.setToolTipText(MessageManager.getString("action.save"));
1114
1115     int value = chooser.showSaveDialog(this);
1116
1117     if (value == JalviewFileChooser.APPROVE_OPTION)
1118     {
1119       currentFileFormat = chooser.getSelectedFormat();
1120       while (currentFileFormat == null)
1121       {
1122         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1123                 MessageManager.getString(
1124                         "label.select_file_format_before_saving"),
1125                 MessageManager.getString("label.file_format_not_specified"),
1126                 JvOptionPane.WARNING_MESSAGE);
1127         currentFileFormat = chooser.getSelectedFormat();
1128         value = chooser.showSaveDialog(this);
1129         if (value != JalviewFileChooser.APPROVE_OPTION)
1130         {
1131           return;
1132         }
1133       }
1134
1135       fileName = chooser.getSelectedFile().getPath();
1136
1137       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1138
1139       Cache.setProperty("LAST_DIRECTORY", fileName);
1140       saveAlignment(fileName, currentFileFormat);
1141     }
1142   }
1143
1144   public boolean saveAlignment(String file, FileFormatI format)
1145   {
1146     boolean success = true;
1147
1148     if (FileFormat.Jalview.equals(format))
1149     {
1150       String shortName = title;
1151
1152       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1153       {
1154         shortName = shortName.substring(
1155                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1156       }
1157
1158       success = new Jalview2XML().saveAlignment(this, file, shortName);
1159
1160       statusBar.setText(MessageManager.formatMessage(
1161               "label.successfully_saved_to_file_in_format", new Object[]
1162               { fileName, format }));
1163
1164     }
1165     else
1166     {
1167       AlignmentExportData exportData = getAlignmentForExport(format,
1168               viewport, null);
1169       if (exportData.getSettings().isCancelled())
1170       {
1171         return false;
1172       }
1173       FormatAdapter f = new FormatAdapter(alignPanel,
1174               exportData.getSettings());
1175       String output = f.formatSequences(format, exportData.getAlignment(), // class
1176                                                                            // cast
1177                                                                            // exceptions
1178                                                                            // will
1179               // occur in the distant future
1180               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1181               f.getCacheSuffixDefault(format),
1182               viewport.getAlignment().getHiddenColumns());
1183
1184       if (output == null)
1185       {
1186         success = false;
1187       }
1188       else
1189       {
1190         try
1191         {
1192           PrintWriter out = new PrintWriter(new FileWriter(file));
1193
1194           out.print(output);
1195           out.close();
1196           this.setTitle(file);
1197           statusBar.setText(MessageManager.formatMessage(
1198                   "label.successfully_saved_to_file_in_format", new Object[]
1199                   { fileName, format.getName() }));
1200         } catch (Exception ex)
1201         {
1202           success = false;
1203           ex.printStackTrace();
1204         }
1205       }
1206     }
1207
1208     if (!success)
1209     {
1210       JvOptionPane.showInternalMessageDialog(this, MessageManager
1211               .formatMessage("label.couldnt_save_file", new Object[]
1212               { fileName }),
1213               MessageManager.getString("label.error_saving_file"),
1214               JvOptionPane.WARNING_MESSAGE);
1215     }
1216
1217     return success;
1218   }
1219
1220   private void warningMessage(String warning, String title)
1221   {
1222     if (new jalview.util.Platform().isHeadless())
1223     {
1224       System.err.println("Warning: " + title + "\nWarning: " + warning);
1225
1226     }
1227     else
1228     {
1229       JvOptionPane.showInternalMessageDialog(this, warning, title,
1230               JvOptionPane.WARNING_MESSAGE);
1231     }
1232     return;
1233   }
1234
1235   /**
1236    * DOCUMENT ME!
1237    *
1238    * @param e
1239    *          DOCUMENT ME!
1240    */
1241   @Override
1242   protected void outputText_actionPerformed(ActionEvent e)
1243   {
1244     FileFormatI fileFormat = FileFormats.getInstance()
1245             .forName(e.getActionCommand());
1246     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1247             viewport, null);
1248     if (exportData.getSettings().isCancelled())
1249     {
1250       return;
1251     }
1252     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1253     cap.setForInput(null);
1254     try
1255     {
1256       FileFormatI format = fileFormat;
1257       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1258               .formatSequences(format, exportData.getAlignment(),
1259                       exportData.getOmitHidden(),
1260                       exportData.getStartEndPostions(),
1261                       viewport.getAlignment().getHiddenColumns()));
1262       Desktop.addInternalFrame(cap, MessageManager
1263               .formatMessage("label.alignment_output_command", new Object[]
1264               { e.getActionCommand() }), 600, 500);
1265     } catch (OutOfMemoryError oom)
1266     {
1267       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1268               oom);
1269       cap.dispose();
1270     }
1271
1272   }
1273
1274   public static AlignmentExportData getAlignmentForExport(
1275           FileFormatI format, AlignViewportI viewport,
1276           AlignExportSettingI exportSettings)
1277   {
1278     AlignmentI alignmentToExport = null;
1279     AlignExportSettingI settings = exportSettings;
1280     String[] omitHidden = null;
1281
1282     HiddenSequences hiddenSeqs = viewport.getAlignment()
1283             .getHiddenSequences();
1284
1285     alignmentToExport = viewport.getAlignment();
1286
1287     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1288     if (settings == null)
1289     {
1290       settings = new AlignExportSettings(hasHiddenSeqs,
1291               viewport.hasHiddenColumns(), format);
1292     }
1293     // settings.isExportAnnotations();
1294
1295     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1296     {
1297       omitHidden = viewport.getViewAsString(false,
1298               settings.isExportHiddenSequences());
1299     }
1300
1301     int[] alignmentStartEnd = new int[2];
1302     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1303     {
1304       alignmentToExport = hiddenSeqs.getFullAlignment();
1305     }
1306     else
1307     {
1308       alignmentToExport = viewport.getAlignment();
1309     }
1310     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1311             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1312     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1313             omitHidden, alignmentStartEnd, settings);
1314     return ed;
1315   }
1316
1317   /**
1318    * DOCUMENT ME!
1319    *
1320    * @param e
1321    *          DOCUMENT ME!
1322    */
1323   @Override
1324   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1325   {
1326     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1327     htmlSVG.exportHTML(null);
1328   }
1329
1330   @Override
1331   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1332   {
1333     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1334     bjs.exportHTML(null);
1335   }
1336
1337   public void createImageMap(File file, String image)
1338   {
1339     alignPanel.makePNGImageMap(file, image);
1340   }
1341
1342   /**
1343    * DOCUMENT ME!
1344    *
1345    * @param e
1346    *          DOCUMENT ME!
1347    */
1348   @Override
1349   public void createPNG(File f)
1350   {
1351     alignPanel.makePNG(f);
1352   }
1353
1354   /**
1355    * DOCUMENT ME!
1356    *
1357    * @param e
1358    *          DOCUMENT ME!
1359    */
1360   @Override
1361   public void createEPS(File f)
1362   {
1363     alignPanel.makeEPS(f);
1364   }
1365
1366   @Override
1367   public void createSVG(File f)
1368   {
1369     alignPanel.makeSVG(f);
1370   }
1371
1372   @Override
1373   public void pageSetup_actionPerformed(ActionEvent e)
1374   {
1375     PrinterJob printJob = PrinterJob.getPrinterJob();
1376     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1377   }
1378
1379   /**
1380    * DOCUMENT ME!
1381    *
1382    * @param e
1383    *          DOCUMENT ME!
1384    */
1385   @Override
1386   public void printMenuItem_actionPerformed(ActionEvent e)
1387   {
1388     // Putting in a thread avoids Swing painting problems
1389     PrintThread thread = new PrintThread(alignPanel);
1390     thread.start();
1391   }
1392
1393   @Override
1394   public void exportFeatures_actionPerformed(ActionEvent e)
1395   {
1396     new AnnotationExporter(alignPanel).exportFeatures();
1397   }
1398
1399   @Override
1400   public void exportAnnotations_actionPerformed(ActionEvent e)
1401   {
1402     new AnnotationExporter(alignPanel).exportAnnotations();
1403   }
1404
1405   @Override
1406   public void associatedData_actionPerformed(ActionEvent e)
1407   {
1408     // Pick the tree file
1409     JalviewFileChooser chooser = new JalviewFileChooser(
1410             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1411     chooser.setFileView(new JalviewFileView());
1412     chooser.setDialogTitle(
1413             MessageManager.getString("label.load_jalview_annotations"));
1414     chooser.setToolTipText(
1415             MessageManager.getString("label.load_jalview_annotations"));
1416
1417     int value = chooser.showOpenDialog(null);
1418
1419     if (value == JalviewFileChooser.APPROVE_OPTION)
1420     {
1421       String choice = chooser.getSelectedFile().getPath();
1422       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1423       loadJalviewDataFile(choice, null, null, null);
1424     }
1425
1426   }
1427
1428   /**
1429    * Close the current view or all views in the alignment frame. If the frame
1430    * only contains one view then the alignment will be removed from memory.
1431    *
1432    * @param closeAllTabs
1433    */
1434   @Override
1435   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1436   {
1437     if (alignPanels != null && alignPanels.size() < 2)
1438     {
1439       closeAllTabs = true;
1440     }
1441
1442     try
1443     {
1444       if (alignPanels != null)
1445       {
1446         if (closeAllTabs)
1447         {
1448           if (this.isClosed())
1449           {
1450             // really close all the windows - otherwise wait till
1451             // setClosed(true) is called
1452             for (int i = 0; i < alignPanels.size(); i++)
1453             {
1454               AlignmentPanel ap = alignPanels.get(i);
1455               ap.closePanel();
1456             }
1457           }
1458         }
1459         else
1460         {
1461           closeView(alignPanel);
1462         }
1463       }
1464
1465       if (closeAllTabs)
1466       {
1467         /*
1468          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1469          * be called recursively, with the frame now in 'closed' state
1470          */
1471         this.setClosed(true);
1472       }
1473     } catch (Exception ex)
1474     {
1475       ex.printStackTrace();
1476     }
1477   }
1478
1479   /**
1480    * Close the specified panel and close up tabs appropriately.
1481    *
1482    * @param panelToClose
1483    */
1484   public void closeView(AlignmentPanel panelToClose)
1485   {
1486     int index = tabbedPane.getSelectedIndex();
1487     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1488     alignPanels.remove(panelToClose);
1489     panelToClose.closePanel();
1490     panelToClose = null;
1491
1492     tabbedPane.removeTabAt(closedindex);
1493     tabbedPane.validate();
1494
1495     if (index > closedindex || index == tabbedPane.getTabCount())
1496     {
1497       // modify currently selected tab index if necessary.
1498       index--;
1499     }
1500
1501     this.tabSelectionChanged(index);
1502   }
1503
1504   /**
1505    * DOCUMENT ME!
1506    */
1507   void updateEditMenuBar()
1508   {
1509
1510     if (viewport.getHistoryList().size() > 0)
1511     {
1512       undoMenuItem.setEnabled(true);
1513       CommandI command = viewport.getHistoryList().peek();
1514       undoMenuItem.setText(MessageManager
1515               .formatMessage("label.undo_command", new Object[]
1516               { command.getDescription() }));
1517     }
1518     else
1519     {
1520       undoMenuItem.setEnabled(false);
1521       undoMenuItem.setText(MessageManager.getString("action.undo"));
1522     }
1523
1524     if (viewport.getRedoList().size() > 0)
1525     {
1526       redoMenuItem.setEnabled(true);
1527
1528       CommandI command = viewport.getRedoList().peek();
1529       redoMenuItem.setText(MessageManager
1530               .formatMessage("label.redo_command", new Object[]
1531               { command.getDescription() }));
1532     }
1533     else
1534     {
1535       redoMenuItem.setEnabled(false);
1536       redoMenuItem.setText(MessageManager.getString("action.redo"));
1537     }
1538   }
1539
1540   @Override
1541   public void addHistoryItem(CommandI command)
1542   {
1543     if (command.getSize() > 0)
1544     {
1545       viewport.addToHistoryList(command);
1546       viewport.clearRedoList();
1547       updateEditMenuBar();
1548       viewport.updateHiddenColumns();
1549       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1550       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1551       // viewport.getColumnSelection()
1552       // .getHiddenColumns().size() > 0);
1553     }
1554   }
1555
1556   /**
1557    *
1558    * @return alignment objects for all views
1559    */
1560   AlignmentI[] getViewAlignments()
1561   {
1562     if (alignPanels != null)
1563     {
1564       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1565       int i = 0;
1566       for (AlignmentPanel ap : alignPanels)
1567       {
1568         als[i++] = ap.av.getAlignment();
1569       }
1570       return als;
1571     }
1572     if (viewport != null)
1573     {
1574       return new AlignmentI[] { viewport.getAlignment() };
1575     }
1576     return null;
1577   }
1578
1579   /**
1580    * DOCUMENT ME!
1581    *
1582    * @param e
1583    *          DOCUMENT ME!
1584    */
1585   @Override
1586   protected void undoMenuItem_actionPerformed(ActionEvent e)
1587   {
1588     if (viewport.getHistoryList().isEmpty())
1589     {
1590       return;
1591     }
1592     CommandI command = viewport.getHistoryList().pop();
1593     viewport.addToRedoList(command);
1594     command.undoCommand(getViewAlignments());
1595
1596     AlignmentViewport originalSource = getOriginatingSource(command);
1597     updateEditMenuBar();
1598
1599     if (originalSource != null)
1600     {
1601       if (originalSource != viewport)
1602       {
1603         Cache.log.warn(
1604                 "Implementation worry: mismatch of viewport origin for undo");
1605       }
1606       originalSource.updateHiddenColumns();
1607       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1608       // null
1609       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1610       // viewport.getColumnSelection()
1611       // .getHiddenColumns().size() > 0);
1612       originalSource.firePropertyChange("alignment", null,
1613               originalSource.getAlignment().getSequences());
1614     }
1615   }
1616
1617   /**
1618    * DOCUMENT ME!
1619    *
1620    * @param e
1621    *          DOCUMENT ME!
1622    */
1623   @Override
1624   protected void redoMenuItem_actionPerformed(ActionEvent e)
1625   {
1626     if (viewport.getRedoList().size() < 1)
1627     {
1628       return;
1629     }
1630
1631     CommandI command = viewport.getRedoList().pop();
1632     viewport.addToHistoryList(command);
1633     command.doCommand(getViewAlignments());
1634
1635     AlignmentViewport originalSource = getOriginatingSource(command);
1636     updateEditMenuBar();
1637
1638     if (originalSource != null)
1639     {
1640
1641       if (originalSource != viewport)
1642       {
1643         Cache.log.warn(
1644                 "Implementation worry: mismatch of viewport origin for redo");
1645       }
1646       originalSource.updateHiddenColumns();
1647       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1648       // null
1649       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1650       // viewport.getColumnSelection()
1651       // .getHiddenColumns().size() > 0);
1652       originalSource.firePropertyChange("alignment", null,
1653               originalSource.getAlignment().getSequences());
1654     }
1655   }
1656
1657   AlignmentViewport getOriginatingSource(CommandI command)
1658   {
1659     AlignmentViewport originalSource = null;
1660     // For sequence removal and addition, we need to fire
1661     // the property change event FROM the viewport where the
1662     // original alignment was altered
1663     AlignmentI al = null;
1664     if (command instanceof EditCommand)
1665     {
1666       EditCommand editCommand = (EditCommand) command;
1667       al = editCommand.getAlignment();
1668       List<Component> comps = PaintRefresher.components
1669               .get(viewport.getSequenceSetId());
1670
1671       for (Component comp : comps)
1672       {
1673         if (comp instanceof AlignmentPanel)
1674         {
1675           if (al == ((AlignmentPanel) comp).av.getAlignment())
1676           {
1677             originalSource = ((AlignmentPanel) comp).av;
1678             break;
1679           }
1680         }
1681       }
1682     }
1683
1684     if (originalSource == null)
1685     {
1686       // The original view is closed, we must validate
1687       // the current view against the closed view first
1688       if (al != null)
1689       {
1690         PaintRefresher.validateSequences(al, viewport.getAlignment());
1691       }
1692
1693       originalSource = viewport;
1694     }
1695
1696     return originalSource;
1697   }
1698
1699   /**
1700    * DOCUMENT ME!
1701    *
1702    * @param up
1703    *          DOCUMENT ME!
1704    */
1705   public void moveSelectedSequences(boolean up)
1706   {
1707     SequenceGroup sg = viewport.getSelectionGroup();
1708
1709     if (sg == null)
1710     {
1711       return;
1712     }
1713     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1714             viewport.getHiddenRepSequences(), up);
1715     alignPanel.paintAlignment(true, false);
1716   }
1717
1718   synchronized void slideSequences(boolean right, int size)
1719   {
1720     List<SequenceI> sg = new ArrayList<>();
1721     if (viewport.cursorMode)
1722     {
1723       sg.add(viewport.getAlignment()
1724               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1725     }
1726     else if (viewport.getSelectionGroup() != null
1727             && viewport.getSelectionGroup().getSize() != viewport
1728                     .getAlignment().getHeight())
1729     {
1730       sg = viewport.getSelectionGroup()
1731               .getSequences(viewport.getHiddenRepSequences());
1732     }
1733
1734     if (sg.size() < 1)
1735     {
1736       return;
1737     }
1738
1739     List<SequenceI> invertGroup = new ArrayList<>();
1740
1741     for (SequenceI seq : viewport.getAlignment().getSequences())
1742     {
1743       if (!sg.contains(seq))
1744       {
1745         invertGroup.add(seq);
1746       }
1747     }
1748
1749     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1750
1751     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1752     for (int i = 0; i < invertGroup.size(); i++)
1753     {
1754       seqs2[i] = invertGroup.get(i);
1755     }
1756
1757     SlideSequencesCommand ssc;
1758     if (right)
1759     {
1760       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1761               viewport.getGapCharacter());
1762     }
1763     else
1764     {
1765       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1766               viewport.getGapCharacter());
1767     }
1768
1769     int groupAdjustment = 0;
1770     if (ssc.getGapsInsertedBegin() && right)
1771     {
1772       if (viewport.cursorMode)
1773       {
1774         alignPanel.getSeqPanel().moveCursor(size, 0);
1775       }
1776       else
1777       {
1778         groupAdjustment = size;
1779       }
1780     }
1781     else if (!ssc.getGapsInsertedBegin() && !right)
1782     {
1783       if (viewport.cursorMode)
1784       {
1785         alignPanel.getSeqPanel().moveCursor(-size, 0);
1786       }
1787       else
1788       {
1789         groupAdjustment = -size;
1790       }
1791     }
1792
1793     if (groupAdjustment != 0)
1794     {
1795       viewport.getSelectionGroup().setStartRes(
1796               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1797       viewport.getSelectionGroup().setEndRes(
1798               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1799     }
1800
1801     /*
1802      * just extend the last slide command if compatible; but not if in
1803      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1804      */
1805     boolean appendHistoryItem = false;
1806     Deque<CommandI> historyList = viewport.getHistoryList();
1807     boolean inSplitFrame = getSplitViewContainer() != null;
1808     if (!inSplitFrame && historyList != null && historyList.size() > 0
1809             && historyList.peek() instanceof SlideSequencesCommand)
1810     {
1811       appendHistoryItem = ssc.appendSlideCommand(
1812               (SlideSequencesCommand) historyList.peek());
1813     }
1814
1815     if (!appendHistoryItem)
1816     {
1817       addHistoryItem(ssc);
1818     }
1819
1820     repaint();
1821   }
1822
1823   /**
1824    * DOCUMENT ME!
1825    *
1826    * @param e
1827    *          DOCUMENT ME!
1828    */
1829   @Override
1830   protected void copy_actionPerformed(ActionEvent e)
1831   {
1832     if (viewport.getSelectionGroup() == null)
1833     {
1834       return;
1835     }
1836     // TODO: preserve the ordering of displayed alignment annotation in any
1837     // internal paste (particularly sequence associated annotation)
1838     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1839     String[] omitHidden = null;
1840
1841     if (viewport.hasHiddenColumns())
1842     {
1843       omitHidden = viewport.getViewAsString(true);
1844     }
1845
1846     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1847             seqs, omitHidden, null);
1848
1849     StringSelection ss = new StringSelection(output);
1850
1851     try
1852     {
1853       jalview.gui.Desktop.internalCopy = true;
1854       // Its really worth setting the clipboard contents
1855       // to empty before setting the large StringSelection!!
1856       Toolkit.getDefaultToolkit().getSystemClipboard()
1857               .setContents(new StringSelection(""), null);
1858
1859       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1860               Desktop.instance);
1861     } catch (OutOfMemoryError er)
1862     {
1863       new OOMWarning("copying region", er);
1864       return;
1865     }
1866
1867     HiddenColumns hiddenColumns = null;
1868     if (viewport.hasHiddenColumns())
1869     {
1870       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1871       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1872
1873       // create new HiddenColumns object with copy of hidden regions
1874       // between startRes and endRes, offset by startRes
1875       hiddenColumns = new HiddenColumns(
1876               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1877               hiddenCutoff, hiddenOffset);
1878     }
1879
1880     Desktop.jalviewClipboard = new Object[] { seqs,
1881         viewport.getAlignment().getDataset(), hiddenColumns };
1882     statusBar.setText(MessageManager.formatMessage(
1883             "label.copied_sequences_to_clipboard", new Object[]
1884             { Integer.valueOf(seqs.length).toString() }));
1885   }
1886
1887   /**
1888    * DOCUMENT ME!
1889    *
1890    * @param e
1891    *          DOCUMENT ME!
1892    */
1893   @Override
1894   protected void pasteNew_actionPerformed(ActionEvent e)
1895   {
1896     paste(true);
1897   }
1898
1899   /**
1900    * DOCUMENT ME!
1901    *
1902    * @param e
1903    *          DOCUMENT ME!
1904    */
1905   @Override
1906   protected void pasteThis_actionPerformed(ActionEvent e)
1907   {
1908     paste(false);
1909   }
1910
1911   /**
1912    * Paste contents of Jalview clipboard
1913    *
1914    * @param newAlignment
1915    *          true to paste to a new alignment, otherwise add to this.
1916    */
1917   void paste(boolean newAlignment)
1918   {
1919     boolean externalPaste = true;
1920     try
1921     {
1922       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1923       Transferable contents = c.getContents(this);
1924
1925       if (contents == null)
1926       {
1927         return;
1928       }
1929
1930       String str;
1931       FileFormatI format;
1932       try
1933       {
1934         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1935         if (str.length() < 1)
1936         {
1937           return;
1938         }
1939
1940         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1941
1942       } catch (OutOfMemoryError er)
1943       {
1944         new OOMWarning("Out of memory pasting sequences!!", er);
1945         return;
1946       }
1947
1948       SequenceI[] sequences;
1949       boolean annotationAdded = false;
1950       AlignmentI alignment = null;
1951
1952       if (Desktop.jalviewClipboard != null)
1953       {
1954         // The clipboard was filled from within Jalview, we must use the
1955         // sequences
1956         // And dataset from the copied alignment
1957         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1958         // be doubly sure that we create *new* sequence objects.
1959         sequences = new SequenceI[newseq.length];
1960         for (int i = 0; i < newseq.length; i++)
1961         {
1962           sequences[i] = new Sequence(newseq[i]);
1963         }
1964         alignment = new Alignment(sequences);
1965         externalPaste = false;
1966       }
1967       else
1968       {
1969         // parse the clipboard as an alignment.
1970         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1971                 format);
1972         sequences = alignment.getSequencesArray();
1973       }
1974
1975       int alwidth = 0;
1976       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1977       int fgroup = -1;
1978
1979       if (newAlignment)
1980       {
1981
1982         if (Desktop.jalviewClipboard != null)
1983         {
1984           // dataset is inherited
1985           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1986         }
1987         else
1988         {
1989           // new dataset is constructed
1990           alignment.setDataset(null);
1991         }
1992         alwidth = alignment.getWidth() + 1;
1993       }
1994       else
1995       {
1996         AlignmentI pastedal = alignment; // preserve pasted alignment object
1997         // Add pasted sequences and dataset into existing alignment.
1998         alignment = viewport.getAlignment();
1999         alwidth = alignment.getWidth() + 1;
2000         // decide if we need to import sequences from an existing dataset
2001         boolean importDs = Desktop.jalviewClipboard != null
2002                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2003         // importDs==true instructs us to copy over new dataset sequences from
2004         // an existing alignment
2005         Vector newDs = (importDs) ? new Vector() : null; // used to create
2006         // minimum dataset set
2007
2008         for (int i = 0; i < sequences.length; i++)
2009         {
2010           if (importDs)
2011           {
2012             newDs.addElement(null);
2013           }
2014           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2015           // paste
2016           if (importDs && ds != null)
2017           {
2018             if (!newDs.contains(ds))
2019             {
2020               newDs.setElementAt(ds, i);
2021               ds = new Sequence(ds);
2022               // update with new dataset sequence
2023               sequences[i].setDatasetSequence(ds);
2024             }
2025             else
2026             {
2027               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2028             }
2029           }
2030           else
2031           {
2032             // copy and derive new dataset sequence
2033             sequences[i] = sequences[i].deriveSequence();
2034             alignment.getDataset()
2035                     .addSequence(sequences[i].getDatasetSequence());
2036             // TODO: avoid creation of duplicate dataset sequences with a
2037             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2038           }
2039           alignment.addSequence(sequences[i]); // merges dataset
2040         }
2041         if (newDs != null)
2042         {
2043           newDs.clear(); // tidy up
2044         }
2045         if (alignment.getAlignmentAnnotation() != null)
2046         {
2047           for (AlignmentAnnotation alan : alignment
2048                   .getAlignmentAnnotation())
2049           {
2050             if (alan.graphGroup > fgroup)
2051             {
2052               fgroup = alan.graphGroup;
2053             }
2054           }
2055         }
2056         if (pastedal.getAlignmentAnnotation() != null)
2057         {
2058           // Add any annotation attached to alignment.
2059           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2060           for (int i = 0; i < alann.length; i++)
2061           {
2062             annotationAdded = true;
2063             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2064             {
2065               AlignmentAnnotation newann = new AlignmentAnnotation(
2066                       alann[i]);
2067               if (newann.graphGroup > -1)
2068               {
2069                 if (newGraphGroups.size() <= newann.graphGroup
2070                         || newGraphGroups.get(newann.graphGroup) == null)
2071                 {
2072                   for (int q = newGraphGroups
2073                           .size(); q <= newann.graphGroup; q++)
2074                   {
2075                     newGraphGroups.add(q, null);
2076                   }
2077                   newGraphGroups.set(newann.graphGroup,
2078                           new Integer(++fgroup));
2079                 }
2080                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2081                         .intValue();
2082               }
2083
2084               newann.padAnnotation(alwidth);
2085               alignment.addAnnotation(newann);
2086             }
2087           }
2088         }
2089       }
2090       if (!newAlignment)
2091       {
2092         // /////
2093         // ADD HISTORY ITEM
2094         //
2095         addHistoryItem(new EditCommand(
2096                 MessageManager.getString("label.add_sequences"),
2097                 Action.PASTE, sequences, 0, alignment.getWidth(),
2098                 alignment));
2099       }
2100       // Add any annotations attached to sequences
2101       for (int i = 0; i < sequences.length; i++)
2102       {
2103         if (sequences[i].getAnnotation() != null)
2104         {
2105           AlignmentAnnotation newann;
2106           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2107           {
2108             annotationAdded = true;
2109             newann = sequences[i].getAnnotation()[a];
2110             newann.adjustForAlignment();
2111             newann.padAnnotation(alwidth);
2112             if (newann.graphGroup > -1)
2113             {
2114               if (newann.graphGroup > -1)
2115               {
2116                 if (newGraphGroups.size() <= newann.graphGroup
2117                         || newGraphGroups.get(newann.graphGroup) == null)
2118                 {
2119                   for (int q = newGraphGroups
2120                           .size(); q <= newann.graphGroup; q++)
2121                   {
2122                     newGraphGroups.add(q, null);
2123                   }
2124                   newGraphGroups.set(newann.graphGroup,
2125                           new Integer(++fgroup));
2126                 }
2127                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2128                         .intValue();
2129               }
2130             }
2131             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2132             // was
2133             // duplicated
2134             // earlier
2135             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2136                     a);
2137           }
2138         }
2139       }
2140       if (!newAlignment)
2141       {
2142
2143         // propagate alignment changed.
2144         viewport.getRanges().setEndSeq(alignment.getHeight());
2145         if (annotationAdded)
2146         {
2147           // Duplicate sequence annotation in all views.
2148           AlignmentI[] alview = this.getViewAlignments();
2149           for (int i = 0; i < sequences.length; i++)
2150           {
2151             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2152             if (sann == null)
2153             {
2154               continue;
2155             }
2156             for (int avnum = 0; avnum < alview.length; avnum++)
2157             {
2158               if (alview[avnum] != alignment)
2159               {
2160                 // duplicate in a view other than the one with input focus
2161                 int avwidth = alview[avnum].getWidth() + 1;
2162                 // this relies on sann being preserved after we
2163                 // modify the sequence's annotation array for each duplication
2164                 for (int a = 0; a < sann.length; a++)
2165                 {
2166                   AlignmentAnnotation newann = new AlignmentAnnotation(
2167                           sann[a]);
2168                   sequences[i].addAlignmentAnnotation(newann);
2169                   newann.padAnnotation(avwidth);
2170                   alview[avnum].addAnnotation(newann); // annotation was
2171                   // duplicated earlier
2172                   // TODO JAL-1145 graphGroups are not updated for sequence
2173                   // annotation added to several views. This may cause
2174                   // strangeness
2175                   alview[avnum].setAnnotationIndex(newann, a);
2176                 }
2177               }
2178             }
2179           }
2180           buildSortByAnnotationScoresMenu();
2181         }
2182         viewport.firePropertyChange("alignment", null,
2183                 alignment.getSequences());
2184         if (alignPanels != null)
2185         {
2186           for (AlignmentPanel ap : alignPanels)
2187           {
2188             ap.validateAnnotationDimensions(false);
2189           }
2190         }
2191         else
2192         {
2193           alignPanel.validateAnnotationDimensions(false);
2194         }
2195
2196       }
2197       else
2198       {
2199         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2200                 DEFAULT_HEIGHT);
2201         String newtitle = new String("Copied sequences");
2202
2203         if (Desktop.jalviewClipboard != null
2204                 && Desktop.jalviewClipboard[2] != null)
2205         {
2206           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2207           af.viewport.setHiddenColumns(hc);
2208         }
2209
2210         // >>>This is a fix for the moment, until a better solution is
2211         // found!!<<<
2212         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2213                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2214                         .getFeatureRenderer());
2215
2216         // TODO: maintain provenance of an alignment, rather than just make the
2217         // title a concatenation of operations.
2218         if (!externalPaste)
2219         {
2220           if (title.startsWith("Copied sequences"))
2221           {
2222             newtitle = title;
2223           }
2224           else
2225           {
2226             newtitle = newtitle.concat("- from " + title);
2227           }
2228         }
2229         else
2230         {
2231           newtitle = new String("Pasted sequences");
2232         }
2233
2234         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2235                 DEFAULT_HEIGHT);
2236
2237       }
2238
2239     } catch (Exception ex)
2240     {
2241       ex.printStackTrace();
2242       System.out.println("Exception whilst pasting: " + ex);
2243       // could be anything being pasted in here
2244     }
2245
2246   }
2247
2248   @Override
2249   protected void expand_newalign(ActionEvent e)
2250   {
2251     try
2252     {
2253       AlignmentI alignment = AlignmentUtils
2254               .expandContext(getViewport().getAlignment(), -1);
2255       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2256               DEFAULT_HEIGHT);
2257       String newtitle = new String("Flanking alignment");
2258
2259       if (Desktop.jalviewClipboard != null
2260               && Desktop.jalviewClipboard[2] != null)
2261       {
2262         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2263         af.viewport.setHiddenColumns(hc);
2264       }
2265
2266       // >>>This is a fix for the moment, until a better solution is
2267       // found!!<<<
2268       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2269               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2270                       .getFeatureRenderer());
2271
2272       // TODO: maintain provenance of an alignment, rather than just make the
2273       // title a concatenation of operations.
2274       {
2275         if (title.startsWith("Copied sequences"))
2276         {
2277           newtitle = title;
2278         }
2279         else
2280         {
2281           newtitle = newtitle.concat("- from " + title);
2282         }
2283       }
2284
2285       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2286
2287     } catch (Exception ex)
2288     {
2289       ex.printStackTrace();
2290       System.out.println("Exception whilst pasting: " + ex);
2291       // could be anything being pasted in here
2292     } catch (OutOfMemoryError oom)
2293     {
2294       new OOMWarning("Viewing flanking region of alignment", oom);
2295     }
2296   }
2297
2298   /**
2299    * DOCUMENT ME!
2300    *
2301    * @param e
2302    *          DOCUMENT ME!
2303    */
2304   @Override
2305   protected void cut_actionPerformed(ActionEvent e)
2306   {
2307     copy_actionPerformed(null);
2308     delete_actionPerformed(null);
2309   }
2310
2311   /**
2312    * DOCUMENT ME!
2313    *
2314    * @param e
2315    *          DOCUMENT ME!
2316    */
2317   @Override
2318   protected void delete_actionPerformed(ActionEvent evt)
2319   {
2320
2321     SequenceGroup sg = viewport.getSelectionGroup();
2322     if (sg == null)
2323     {
2324       return;
2325     }
2326
2327     /*
2328      * If the cut affects all sequences, warn, remove highlighted columns
2329      */
2330     if (sg.getSize() == viewport.getAlignment().getHeight())
2331     {
2332       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2333               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2334       if (isEntireAlignWidth)
2335       {
2336         int confirm = JvOptionPane.showConfirmDialog(this,
2337                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2338                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2339                 JvOptionPane.OK_CANCEL_OPTION);
2340
2341         if (confirm == JvOptionPane.CANCEL_OPTION
2342                 || confirm == JvOptionPane.CLOSED_OPTION)
2343         {
2344           return;
2345         }
2346       }
2347       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2348               sg.getEndRes() + 1);
2349     }
2350     SequenceI[] cut = sg.getSequences()
2351             .toArray(new SequenceI[sg.getSize()]);
2352
2353     addHistoryItem(new EditCommand(
2354             MessageManager.getString("label.cut_sequences"), Action.CUT,
2355             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2356             viewport.getAlignment()));
2357
2358     viewport.setSelectionGroup(null);
2359     viewport.sendSelection();
2360     viewport.getAlignment().deleteGroup(sg);
2361
2362     viewport.firePropertyChange("alignment", null,
2363             viewport.getAlignment().getSequences());
2364     if (viewport.getAlignment().getHeight() < 1)
2365     {
2366       try
2367       {
2368         this.setClosed(true);
2369       } catch (Exception ex)
2370       {
2371       }
2372     }
2373   }
2374
2375   /**
2376    * DOCUMENT ME!
2377    *
2378    * @param e
2379    *          DOCUMENT ME!
2380    */
2381   @Override
2382   protected void deleteGroups_actionPerformed(ActionEvent e)
2383   {
2384     if (avc.deleteGroups())
2385     {
2386       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2387       alignPanel.updateAnnotation();
2388       alignPanel.paintAlignment(true, true);
2389     }
2390   }
2391
2392   /**
2393    * DOCUMENT ME!
2394    *
2395    * @param e
2396    *          DOCUMENT ME!
2397    */
2398   @Override
2399   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2400   {
2401     SequenceGroup sg = new SequenceGroup();
2402
2403     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2404     {
2405       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2406     }
2407
2408     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2409     viewport.setSelectionGroup(sg);
2410     viewport.sendSelection();
2411     // JAL-2034 - should delegate to
2412     // alignPanel to decide if overview needs
2413     // updating.
2414     alignPanel.paintAlignment(false, false);
2415     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2416   }
2417
2418   /**
2419    * DOCUMENT ME!
2420    *
2421    * @param e
2422    *          DOCUMENT ME!
2423    */
2424   @Override
2425   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2426   {
2427     if (viewport.cursorMode)
2428     {
2429       alignPanel.getSeqPanel().keyboardNo1 = null;
2430       alignPanel.getSeqPanel().keyboardNo2 = null;
2431     }
2432     viewport.setSelectionGroup(null);
2433     viewport.getColumnSelection().clear();
2434     viewport.setSelectionGroup(null);
2435     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2436     // JAL-2034 - should delegate to
2437     // alignPanel to decide if overview needs
2438     // updating.
2439     alignPanel.paintAlignment(false, false);
2440     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2441     viewport.sendSelection();
2442   }
2443
2444   /**
2445    * DOCUMENT ME!
2446    *
2447    * @param e
2448    *          DOCUMENT ME!
2449    */
2450   @Override
2451   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2452   {
2453     SequenceGroup sg = viewport.getSelectionGroup();
2454
2455     if (sg == null)
2456     {
2457       selectAllSequenceMenuItem_actionPerformed(null);
2458
2459       return;
2460     }
2461
2462     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2463     {
2464       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2465     }
2466     // JAL-2034 - should delegate to
2467     // alignPanel to decide if overview needs
2468     // updating.
2469
2470     alignPanel.paintAlignment(true, false);
2471     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2472     viewport.sendSelection();
2473   }
2474
2475   @Override
2476   public void invertColSel_actionPerformed(ActionEvent e)
2477   {
2478     viewport.invertColumnSelection();
2479     alignPanel.paintAlignment(true, false);
2480     viewport.sendSelection();
2481   }
2482
2483   /**
2484    * DOCUMENT ME!
2485    *
2486    * @param e
2487    *          DOCUMENT ME!
2488    */
2489   @Override
2490   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2491   {
2492     trimAlignment(true);
2493   }
2494
2495   /**
2496    * DOCUMENT ME!
2497    *
2498    * @param e
2499    *          DOCUMENT ME!
2500    */
2501   @Override
2502   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2503   {
2504     trimAlignment(false);
2505   }
2506
2507   void trimAlignment(boolean trimLeft)
2508   {
2509     ColumnSelection colSel = viewport.getColumnSelection();
2510     int column;
2511
2512     if (!colSel.isEmpty())
2513     {
2514       if (trimLeft)
2515       {
2516         column = colSel.getMin();
2517       }
2518       else
2519       {
2520         column = colSel.getMax();
2521       }
2522
2523       SequenceI[] seqs;
2524       if (viewport.getSelectionGroup() != null)
2525       {
2526         seqs = viewport.getSelectionGroup()
2527                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2528       }
2529       else
2530       {
2531         seqs = viewport.getAlignment().getSequencesArray();
2532       }
2533
2534       TrimRegionCommand trimRegion;
2535       if (trimLeft)
2536       {
2537         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2538                 column, viewport.getAlignment());
2539         viewport.getRanges().setStartRes(0);
2540       }
2541       else
2542       {
2543         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2544                 column, viewport.getAlignment());
2545       }
2546
2547       statusBar.setText(MessageManager
2548               .formatMessage("label.removed_columns", new String[]
2549               { Integer.valueOf(trimRegion.getSize()).toString() }));
2550
2551       addHistoryItem(trimRegion);
2552
2553       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2554       {
2555         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2556                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2557         {
2558           viewport.getAlignment().deleteGroup(sg);
2559         }
2560       }
2561
2562       viewport.firePropertyChange("alignment", null,
2563               viewport.getAlignment().getSequences());
2564     }
2565   }
2566
2567   /**
2568    * DOCUMENT ME!
2569    *
2570    * @param e
2571    *          DOCUMENT ME!
2572    */
2573   @Override
2574   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2575   {
2576     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2577
2578     SequenceI[] seqs;
2579     if (viewport.getSelectionGroup() != null)
2580     {
2581       seqs = viewport.getSelectionGroup()
2582               .getSequencesAsArray(viewport.getHiddenRepSequences());
2583       start = viewport.getSelectionGroup().getStartRes();
2584       end = viewport.getSelectionGroup().getEndRes();
2585     }
2586     else
2587     {
2588       seqs = viewport.getAlignment().getSequencesArray();
2589     }
2590
2591     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2592             "Remove Gapped Columns", seqs, start, end,
2593             viewport.getAlignment());
2594
2595     addHistoryItem(removeGapCols);
2596
2597     statusBar.setText(MessageManager
2598             .formatMessage("label.removed_empty_columns", new Object[]
2599             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2600
2601     // This is to maintain viewport position on first residue
2602     // of first sequence
2603     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2604     ViewportRanges ranges = viewport.getRanges();
2605     int startRes = seq.findPosition(ranges.getStartRes());
2606     // ShiftList shifts;
2607     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2608     // edit.alColumnChanges=shifts.getInverse();
2609     // if (viewport.hasHiddenColumns)
2610     // viewport.getColumnSelection().compensateForEdits(shifts);
2611     ranges.setStartRes(seq.findIndex(startRes) - 1);
2612     viewport.firePropertyChange("alignment", null,
2613             viewport.getAlignment().getSequences());
2614
2615   }
2616
2617   /**
2618    * DOCUMENT ME!
2619    *
2620    * @param e
2621    *          DOCUMENT ME!
2622    */
2623   @Override
2624   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2625   {
2626     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2627
2628     SequenceI[] seqs;
2629     if (viewport.getSelectionGroup() != null)
2630     {
2631       seqs = viewport.getSelectionGroup()
2632               .getSequencesAsArray(viewport.getHiddenRepSequences());
2633       start = viewport.getSelectionGroup().getStartRes();
2634       end = viewport.getSelectionGroup().getEndRes();
2635     }
2636     else
2637     {
2638       seqs = viewport.getAlignment().getSequencesArray();
2639     }
2640
2641     // This is to maintain viewport position on first residue
2642     // of first sequence
2643     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2644     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2645
2646     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2647             viewport.getAlignment()));
2648
2649     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2650
2651     viewport.firePropertyChange("alignment", null,
2652             viewport.getAlignment().getSequences());
2653
2654   }
2655
2656   /**
2657    * DOCUMENT ME!
2658    *
2659    * @param e
2660    *          DOCUMENT ME!
2661    */
2662   @Override
2663   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2664   {
2665     viewport.setPadGaps(padGapsMenuitem.isSelected());
2666     viewport.firePropertyChange("alignment", null,
2667             viewport.getAlignment().getSequences());
2668   }
2669
2670   /**
2671    * DOCUMENT ME!
2672    *
2673    * @param e
2674    *          DOCUMENT ME!
2675    */
2676   @Override
2677   public void findMenuItem_actionPerformed(ActionEvent e)
2678   {
2679     new Finder();
2680   }
2681
2682   /**
2683    * Create a new view of the current alignment.
2684    */
2685   @Override
2686   public void newView_actionPerformed(ActionEvent e)
2687   {
2688     newView(null, true);
2689   }
2690
2691   /**
2692    * Creates and shows a new view of the current alignment.
2693    *
2694    * @param viewTitle
2695    *          title of newly created view; if null, one will be generated
2696    * @param copyAnnotation
2697    *          if true then duplicate all annnotation, groups and settings
2698    * @return new alignment panel, already displayed.
2699    */
2700   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2701   {
2702     /*
2703      * Create a new AlignmentPanel (with its own, new Viewport)
2704      */
2705     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2706     if (!copyAnnotation)
2707     {
2708       /*
2709        * remove all groups and annotation except for the automatic stuff
2710        */
2711       newap.av.getAlignment().deleteAllGroups();
2712       newap.av.getAlignment().deleteAllAnnotations(false);
2713     }
2714
2715     newap.av.setGatherViewsHere(false);
2716
2717     if (viewport.viewName == null)
2718     {
2719       viewport.viewName = MessageManager
2720               .getString("label.view_name_original");
2721     }
2722
2723     /*
2724      * Views share the same edits undo and redo stacks
2725      */
2726     newap.av.setHistoryList(viewport.getHistoryList());
2727     newap.av.setRedoList(viewport.getRedoList());
2728
2729     /*
2730      * Views share the same mappings; need to deregister any new mappings
2731      * created by copyAlignPanel, and register the new reference to the shared
2732      * mappings
2733      */
2734     newap.av.replaceMappings(viewport.getAlignment());
2735
2736     /*
2737      * start up cDNA consensus (if applicable) now mappings are in place
2738      */
2739     if (newap.av.initComplementConsensus())
2740     {
2741       newap.refresh(true); // adjust layout of annotations
2742     }
2743
2744     newap.av.viewName = getNewViewName(viewTitle);
2745
2746     addAlignmentPanel(newap, true);
2747     newap.alignmentChanged();
2748
2749     if (alignPanels.size() == 2)
2750     {
2751       viewport.setGatherViewsHere(true);
2752     }
2753     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2754     return newap;
2755   }
2756
2757   /**
2758    * Make a new name for the view, ensuring it is unique within the current
2759    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2760    * these now use viewId. Unique view names are still desirable for usability.)
2761    *
2762    * @param viewTitle
2763    * @return
2764    */
2765   protected String getNewViewName(String viewTitle)
2766   {
2767     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2768     boolean addFirstIndex = false;
2769     if (viewTitle == null || viewTitle.trim().length() == 0)
2770     {
2771       viewTitle = MessageManager.getString("action.view");
2772       addFirstIndex = true;
2773     }
2774     else
2775     {
2776       index = 1;// we count from 1 if given a specific name
2777     }
2778     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2779
2780     List<Component> comps = PaintRefresher.components
2781             .get(viewport.getSequenceSetId());
2782
2783     List<String> existingNames = getExistingViewNames(comps);
2784
2785     while (existingNames.contains(newViewName))
2786     {
2787       newViewName = viewTitle + " " + (++index);
2788     }
2789     return newViewName;
2790   }
2791
2792   /**
2793    * Returns a list of distinct view names found in the given list of
2794    * components. View names are held on the viewport of an AlignmentPanel.
2795    *
2796    * @param comps
2797    * @return
2798    */
2799   protected List<String> getExistingViewNames(List<Component> comps)
2800   {
2801     List<String> existingNames = new ArrayList<>();
2802     for (Component comp : comps)
2803     {
2804       if (comp instanceof AlignmentPanel)
2805       {
2806         AlignmentPanel ap = (AlignmentPanel) comp;
2807         if (!existingNames.contains(ap.av.viewName))
2808         {
2809           existingNames.add(ap.av.viewName);
2810         }
2811       }
2812     }
2813     return existingNames;
2814   }
2815
2816   /**
2817    * Explode tabbed views into separate windows.
2818    */
2819   @Override
2820   public void expandViews_actionPerformed(ActionEvent e)
2821   {
2822     Desktop.explodeViews(this);
2823   }
2824
2825   /**
2826    * Gather views in separate windows back into a tabbed presentation.
2827    */
2828   @Override
2829   public void gatherViews_actionPerformed(ActionEvent e)
2830   {
2831     Desktop.instance.gatherViews(this);
2832   }
2833
2834   /**
2835    * DOCUMENT ME!
2836    *
2837    * @param e
2838    *          DOCUMENT ME!
2839    */
2840   @Override
2841   public void font_actionPerformed(ActionEvent e)
2842   {
2843     new FontChooser(alignPanel);
2844   }
2845
2846   /**
2847    * DOCUMENT ME!
2848    *
2849    * @param e
2850    *          DOCUMENT ME!
2851    */
2852   @Override
2853   protected void seqLimit_actionPerformed(ActionEvent e)
2854   {
2855     viewport.setShowJVSuffix(seqLimits.isSelected());
2856
2857     alignPanel.getIdPanel().getIdCanvas()
2858             .setPreferredSize(alignPanel.calculateIdWidth());
2859     alignPanel.paintAlignment(true, false);
2860   }
2861
2862   @Override
2863   public void idRightAlign_actionPerformed(ActionEvent e)
2864   {
2865     viewport.setRightAlignIds(idRightAlign.isSelected());
2866     alignPanel.paintAlignment(false, false);
2867   }
2868
2869   @Override
2870   public void centreColumnLabels_actionPerformed(ActionEvent e)
2871   {
2872     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2873     alignPanel.paintAlignment(false, false);
2874   }
2875
2876   /*
2877    * (non-Javadoc)
2878    *
2879    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2880    */
2881   @Override
2882   protected void followHighlight_actionPerformed()
2883   {
2884     /*
2885      * Set the 'follow' flag on the Viewport (and scroll to position if now
2886      * true).
2887      */
2888     final boolean state = this.followHighlightMenuItem.getState();
2889     viewport.setFollowHighlight(state);
2890     if (state)
2891     {
2892       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2893     }
2894   }
2895
2896   /**
2897    * DOCUMENT ME!
2898    *
2899    * @param e
2900    *          DOCUMENT ME!
2901    */
2902   @Override
2903   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2904   {
2905     viewport.setColourText(colourTextMenuItem.isSelected());
2906     alignPanel.paintAlignment(false, false);
2907   }
2908
2909   /**
2910    * DOCUMENT ME!
2911    *
2912    * @param e
2913    *          DOCUMENT ME!
2914    */
2915   @Override
2916   public void wrapMenuItem_actionPerformed(ActionEvent e)
2917   {
2918     scaleAbove.setVisible(wrapMenuItem.isSelected());
2919     scaleLeft.setVisible(wrapMenuItem.isSelected());
2920     scaleRight.setVisible(wrapMenuItem.isSelected());
2921     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2922     alignPanel.updateLayout();
2923   }
2924
2925   @Override
2926   public void showAllSeqs_actionPerformed(ActionEvent e)
2927   {
2928     viewport.showAllHiddenSeqs();
2929   }
2930
2931   @Override
2932   public void showAllColumns_actionPerformed(ActionEvent e)
2933   {
2934     viewport.showAllHiddenColumns();
2935     alignPanel.paintAlignment(true, true);
2936     viewport.sendSelection();
2937   }
2938
2939   @Override
2940   public void hideSelSequences_actionPerformed(ActionEvent e)
2941   {
2942     viewport.hideAllSelectedSeqs();
2943   }
2944
2945   /**
2946    * called by key handler and the hide all/show all menu items
2947    *
2948    * @param toggleSeqs
2949    * @param toggleCols
2950    */
2951   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2952   {
2953
2954     boolean hide = false;
2955     SequenceGroup sg = viewport.getSelectionGroup();
2956     if (!toggleSeqs && !toggleCols)
2957     {
2958       // Hide everything by the current selection - this is a hack - we do the
2959       // invert and then hide
2960       // first check that there will be visible columns after the invert.
2961       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2962               && sg.getStartRes() <= sg.getEndRes()))
2963       {
2964         // now invert the sequence set, if required - empty selection implies
2965         // that no hiding is required.
2966         if (sg != null)
2967         {
2968           invertSequenceMenuItem_actionPerformed(null);
2969           sg = viewport.getSelectionGroup();
2970           toggleSeqs = true;
2971
2972         }
2973         viewport.expandColSelection(sg, true);
2974         // finally invert the column selection and get the new sequence
2975         // selection.
2976         invertColSel_actionPerformed(null);
2977         toggleCols = true;
2978       }
2979     }
2980
2981     if (toggleSeqs)
2982     {
2983       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2984       {
2985         hideSelSequences_actionPerformed(null);
2986         hide = true;
2987       }
2988       else if (!(toggleCols && viewport.hasSelectedColumns()))
2989       {
2990         showAllSeqs_actionPerformed(null);
2991       }
2992     }
2993
2994     if (toggleCols)
2995     {
2996       if (viewport.hasSelectedColumns())
2997       {
2998         hideSelColumns_actionPerformed(null);
2999         if (!toggleSeqs)
3000         {
3001           viewport.setSelectionGroup(sg);
3002         }
3003       }
3004       else if (!hide)
3005       {
3006         showAllColumns_actionPerformed(null);
3007       }
3008     }
3009   }
3010
3011   /*
3012    * (non-Javadoc)
3013    *
3014    * @see
3015    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3016    * event.ActionEvent)
3017    */
3018   @Override
3019   public void hideAllButSelection_actionPerformed(ActionEvent e)
3020   {
3021     toggleHiddenRegions(false, false);
3022     viewport.sendSelection();
3023   }
3024
3025   /*
3026    * (non-Javadoc)
3027    *
3028    * @see
3029    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3030    * .ActionEvent)
3031    */
3032   @Override
3033   public void hideAllSelection_actionPerformed(ActionEvent e)
3034   {
3035     SequenceGroup sg = viewport.getSelectionGroup();
3036     viewport.expandColSelection(sg, false);
3037     viewport.hideAllSelectedSeqs();
3038     viewport.hideSelectedColumns();
3039     alignPanel.paintAlignment(true, true);
3040     viewport.sendSelection();
3041   }
3042
3043   /*
3044    * (non-Javadoc)
3045    *
3046    * @see
3047    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3048    * ActionEvent)
3049    */
3050   @Override
3051   public void showAllhidden_actionPerformed(ActionEvent e)
3052   {
3053     viewport.showAllHiddenColumns();
3054     viewport.showAllHiddenSeqs();
3055     alignPanel.paintAlignment(true, true);
3056     viewport.sendSelection();
3057   }
3058
3059   @Override
3060   public void hideSelColumns_actionPerformed(ActionEvent e)
3061   {
3062     viewport.hideSelectedColumns();
3063     alignPanel.paintAlignment(true, true);
3064     viewport.sendSelection();
3065   }
3066
3067   @Override
3068   public void hiddenMarkers_actionPerformed(ActionEvent e)
3069   {
3070     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3071     repaint();
3072   }
3073
3074   /**
3075    * DOCUMENT ME!
3076    *
3077    * @param e
3078    *          DOCUMENT ME!
3079    */
3080   @Override
3081   protected void scaleAbove_actionPerformed(ActionEvent e)
3082   {
3083     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3084     // TODO: do we actually need to update overview for scale above change ?
3085     alignPanel.paintAlignment(true, false);
3086   }
3087
3088   /**
3089    * DOCUMENT ME!
3090    *
3091    * @param e
3092    *          DOCUMENT ME!
3093    */
3094   @Override
3095   protected void scaleLeft_actionPerformed(ActionEvent e)
3096   {
3097     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3098     alignPanel.paintAlignment(true, false);
3099   }
3100
3101   /**
3102    * DOCUMENT ME!
3103    *
3104    * @param e
3105    *          DOCUMENT ME!
3106    */
3107   @Override
3108   protected void scaleRight_actionPerformed(ActionEvent e)
3109   {
3110     viewport.setScaleRightWrapped(scaleRight.isSelected());
3111     alignPanel.paintAlignment(true, false);
3112   }
3113
3114   /**
3115    * DOCUMENT ME!
3116    *
3117    * @param e
3118    *          DOCUMENT ME!
3119    */
3120   @Override
3121   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3122   {
3123     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3124     alignPanel.paintAlignment(false, false);
3125   }
3126
3127   /**
3128    * DOCUMENT ME!
3129    *
3130    * @param e
3131    *          DOCUMENT ME!
3132    */
3133   @Override
3134   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3135   {
3136     viewport.setShowText(viewTextMenuItem.isSelected());
3137     alignPanel.paintAlignment(false, false);
3138   }
3139
3140   /**
3141    * DOCUMENT ME!
3142    *
3143    * @param e
3144    *          DOCUMENT ME!
3145    */
3146   @Override
3147   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3148   {
3149     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3150     alignPanel.paintAlignment(false, false);
3151   }
3152
3153   public FeatureSettings featureSettings;
3154
3155   @Override
3156   public FeatureSettingsControllerI getFeatureSettingsUI()
3157   {
3158     return featureSettings;
3159   }
3160
3161   @Override
3162   public void featureSettings_actionPerformed(ActionEvent e)
3163   {
3164     if (featureSettings != null)
3165     {
3166       featureSettings.close();
3167       featureSettings = null;
3168     }
3169     if (!showSeqFeatures.isSelected())
3170     {
3171       // make sure features are actually displayed
3172       showSeqFeatures.setSelected(true);
3173       showSeqFeatures_actionPerformed(null);
3174     }
3175     featureSettings = new FeatureSettings(this);
3176   }
3177
3178   /**
3179    * Set or clear 'Show Sequence Features'
3180    *
3181    * @param evt
3182    *          DOCUMENT ME!
3183    */
3184   @Override
3185   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3186   {
3187     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3188     alignPanel.paintAlignment(true, true);
3189   }
3190
3191   /**
3192    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3193    * the annotations panel as a whole.
3194    *
3195    * The options to show/hide all annotations should be enabled when the panel
3196    * is shown, and disabled when the panel is hidden.
3197    *
3198    * @param e
3199    */
3200   @Override
3201   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3202   {
3203     final boolean setVisible = annotationPanelMenuItem.isSelected();
3204     viewport.setShowAnnotation(setVisible);
3205     this.showAllSeqAnnotations.setEnabled(setVisible);
3206     this.hideAllSeqAnnotations.setEnabled(setVisible);
3207     this.showAllAlAnnotations.setEnabled(setVisible);
3208     this.hideAllAlAnnotations.setEnabled(setVisible);
3209     alignPanel.updateLayout();
3210   }
3211
3212   @Override
3213   public void alignmentProperties()
3214   {
3215     JEditorPane editPane = new JEditorPane("text/html", "");
3216     editPane.setEditable(false);
3217     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3218             .formatAsHtml();
3219     editPane.setText(
3220             MessageManager.formatMessage("label.html_content", new Object[]
3221             { contents.toString() }));
3222     JInternalFrame frame = new JInternalFrame();
3223     frame.getContentPane().add(new JScrollPane(editPane));
3224
3225     Desktop.addInternalFrame(frame, MessageManager
3226             .formatMessage("label.alignment_properties", new Object[]
3227             { getTitle() }), 500, 400);
3228   }
3229
3230   /**
3231    * DOCUMENT ME!
3232    *
3233    * @param e
3234    *          DOCUMENT ME!
3235    */
3236   @Override
3237   public void overviewMenuItem_actionPerformed(ActionEvent e)
3238   {
3239     if (alignPanel.overviewPanel != null)
3240     {
3241       return;
3242     }
3243
3244     JInternalFrame frame = new JInternalFrame();
3245     final OverviewPanel overview = new OverviewPanel(alignPanel);
3246     frame.setContentPane(overview);
3247     Desktop.addInternalFrame(frame, MessageManager
3248             .formatMessage("label.overview_params", new Object[]
3249             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3250             true, true);
3251     frame.pack();
3252     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3253     frame.addInternalFrameListener(
3254             new javax.swing.event.InternalFrameAdapter()
3255             {
3256               @Override
3257               public void internalFrameClosed(
3258                       javax.swing.event.InternalFrameEvent evt)
3259               {
3260                 overview.dispose();
3261                 alignPanel.setOverviewPanel(null);
3262               };
3263             });
3264
3265     alignPanel.setOverviewPanel(overview);
3266   }
3267
3268   @Override
3269   public void textColour_actionPerformed()
3270   {
3271     new TextColourChooser().chooseColour(alignPanel, null);
3272   }
3273
3274   /*
3275    * public void covariationColour_actionPerformed() {
3276    * changeColour(new
3277    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3278    * ()[0])); }
3279    */
3280   @Override
3281   public void annotationColour_actionPerformed()
3282   {
3283     new AnnotationColourChooser(viewport, alignPanel);
3284   }
3285
3286   @Override
3287   public void annotationColumn_actionPerformed(ActionEvent e)
3288   {
3289     new AnnotationColumnChooser(viewport, alignPanel);
3290   }
3291
3292   /**
3293    * Action on the user checking or unchecking the option to apply the selected
3294    * colour scheme to all groups. If unchecked, groups may have their own
3295    * independent colour schemes.
3296    *
3297    * @param selected
3298    */
3299   @Override
3300   public void applyToAllGroups_actionPerformed(boolean selected)
3301   {
3302     viewport.setColourAppliesToAllGroups(selected);
3303   }
3304
3305   /**
3306    * Action on user selecting a colour from the colour menu
3307    *
3308    * @param name
3309    *          the name (not the menu item label!) of the colour scheme
3310    */
3311   @Override
3312   public void changeColour_actionPerformed(String name)
3313   {
3314     /*
3315      * 'User Defined' opens a panel to configure or load a
3316      * user-defined colour scheme
3317      */
3318     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3319     {
3320       new UserDefinedColours(alignPanel);
3321       return;
3322     }
3323
3324     /*
3325      * otherwise set the chosen colour scheme (or null for 'None')
3326      */
3327     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3328             viewport.getAlignment(), viewport.getHiddenRepSequences());
3329     changeColour(cs);
3330   }
3331
3332   /**
3333    * Actions on setting or changing the alignment colour scheme
3334    *
3335    * @param cs
3336    */
3337   @Override
3338   public void changeColour(ColourSchemeI cs)
3339   {
3340     // TODO: pull up to controller method
3341     ColourMenuHelper.setColourSelected(colourMenu, cs);
3342
3343     viewport.setGlobalColourScheme(cs);
3344
3345     alignPanel.paintAlignment(true, true);
3346   }
3347
3348   /**
3349    * Show the PID threshold slider panel
3350    */
3351   @Override
3352   protected void modifyPID_actionPerformed()
3353   {
3354     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3355             alignPanel.getViewName());
3356     SliderPanel.showPIDSlider();
3357   }
3358
3359   /**
3360    * Show the Conservation slider panel
3361    */
3362   @Override
3363   protected void modifyConservation_actionPerformed()
3364   {
3365     SliderPanel.setConservationSlider(alignPanel,
3366             viewport.getResidueShading(), alignPanel.getViewName());
3367     SliderPanel.showConservationSlider();
3368   }
3369
3370   /**
3371    * Action on selecting or deselecting (Colour) By Conservation
3372    */
3373   @Override
3374   public void conservationMenuItem_actionPerformed(boolean selected)
3375   {
3376     modifyConservation.setEnabled(selected);
3377     viewport.setConservationSelected(selected);
3378     viewport.getResidueShading().setConservationApplied(selected);
3379
3380     changeColour(viewport.getGlobalColourScheme());
3381     if (selected)
3382     {
3383       modifyConservation_actionPerformed();
3384     }
3385     else
3386     {
3387       SliderPanel.hideConservationSlider();
3388     }
3389   }
3390
3391   /**
3392    * Action on selecting or deselecting (Colour) Above PID Threshold
3393    */
3394   @Override
3395   public void abovePIDThreshold_actionPerformed(boolean selected)
3396   {
3397     modifyPID.setEnabled(selected);
3398     viewport.setAbovePIDThreshold(selected);
3399     if (!selected)
3400     {
3401       viewport.getResidueShading().setThreshold(0,
3402               viewport.isIgnoreGapsConsensus());
3403     }
3404
3405     changeColour(viewport.getGlobalColourScheme());
3406     if (selected)
3407     {
3408       modifyPID_actionPerformed();
3409     }
3410     else
3411     {
3412       SliderPanel.hidePIDSlider();
3413     }
3414   }
3415
3416   /**
3417    * DOCUMENT ME!
3418    *
3419    * @param e
3420    *          DOCUMENT ME!
3421    */
3422   @Override
3423   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3424   {
3425     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3426     AlignmentSorter.sortByPID(viewport.getAlignment(),
3427             viewport.getAlignment().getSequenceAt(0));
3428     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3429             viewport.getAlignment()));
3430     alignPanel.paintAlignment(true, false);
3431   }
3432
3433   /**
3434    * DOCUMENT ME!
3435    *
3436    * @param e
3437    *          DOCUMENT ME!
3438    */
3439   @Override
3440   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3441   {
3442     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3443     AlignmentSorter.sortByID(viewport.getAlignment());
3444     addHistoryItem(
3445             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3446     alignPanel.paintAlignment(true, false);
3447   }
3448
3449   /**
3450    * DOCUMENT ME!
3451    *
3452    * @param e
3453    *          DOCUMENT ME!
3454    */
3455   @Override
3456   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3457   {
3458     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3459     AlignmentSorter.sortByLength(viewport.getAlignment());
3460     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3461             viewport.getAlignment()));
3462     alignPanel.paintAlignment(true, false);
3463   }
3464
3465   /**
3466    * DOCUMENT ME!
3467    *
3468    * @param e
3469    *          DOCUMENT ME!
3470    */
3471   @Override
3472   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3473   {
3474     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3475     AlignmentSorter.sortByGroup(viewport.getAlignment());
3476     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3477             viewport.getAlignment()));
3478
3479     alignPanel.paintAlignment(true, false);
3480   }
3481
3482   /**
3483    * DOCUMENT ME!
3484    *
3485    * @param e
3486    *          DOCUMENT ME!
3487    */
3488   @Override
3489   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3490   {
3491     new RedundancyPanel(alignPanel, this);
3492   }
3493
3494   /**
3495    * DOCUMENT ME!
3496    *
3497    * @param e
3498    *          DOCUMENT ME!
3499    */
3500   @Override
3501   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3502   {
3503     if ((viewport.getSelectionGroup() == null)
3504             || (viewport.getSelectionGroup().getSize() < 2))
3505     {
3506       JvOptionPane.showInternalMessageDialog(this,
3507               MessageManager.getString(
3508                       "label.you_must_select_least_two_sequences"),
3509               MessageManager.getString("label.invalid_selection"),
3510               JvOptionPane.WARNING_MESSAGE);
3511     }
3512     else
3513     {
3514       JInternalFrame frame = new JInternalFrame();
3515       frame.setContentPane(new PairwiseAlignPanel(viewport));
3516       Desktop.addInternalFrame(frame,
3517               MessageManager.getString("action.pairwise_alignment"), 600,
3518               500);
3519     }
3520   }
3521
3522   @Override
3523   public void autoCalculate_actionPerformed(ActionEvent e)
3524   {
3525     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3526     if (viewport.autoCalculateConsensus)
3527     {
3528       viewport.firePropertyChange("alignment", null,
3529               viewport.getAlignment().getSequences());
3530     }
3531   }
3532
3533   @Override
3534   public void sortByTreeOption_actionPerformed(ActionEvent e)
3535   {
3536     viewport.sortByTree = sortByTree.isSelected();
3537   }
3538
3539   @Override
3540   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3541   {
3542     viewport.followSelection = listenToViewSelections.isSelected();
3543   }
3544
3545   /**
3546    * Constructs a tree panel and adds it to the desktop
3547    *
3548    * @param type
3549    *          tree type (NJ or AV)
3550    * @param modelName
3551    *          name of score model used to compute the tree
3552    * @param options
3553    *          parameters for the distance or similarity calculation
3554    */
3555   void newTreePanel(String type, String modelName,
3556           SimilarityParamsI options)
3557   {
3558     String frameTitle = "";
3559     TreePanel tp;
3560
3561     boolean onSelection = false;
3562     if (viewport.getSelectionGroup() != null
3563             && viewport.getSelectionGroup().getSize() > 0)
3564     {
3565       SequenceGroup sg = viewport.getSelectionGroup();
3566
3567       /* Decide if the selection is a column region */
3568       for (SequenceI _s : sg.getSequences())
3569       {
3570         if (_s.getLength() < sg.getEndRes())
3571         {
3572           JvOptionPane.showMessageDialog(Desktop.desktop,
3573                   MessageManager.getString(
3574                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3575                   MessageManager.getString(
3576                           "label.sequences_selection_not_aligned"),
3577                   JvOptionPane.WARNING_MESSAGE);
3578
3579           return;
3580         }
3581       }
3582       onSelection = true;
3583     }
3584     else
3585     {
3586       if (viewport.getAlignment().getHeight() < 2)
3587       {
3588         return;
3589       }
3590     }
3591
3592     tp = new TreePanel(alignPanel, type, modelName, options);
3593     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3594
3595     frameTitle += " from ";
3596
3597     if (viewport.viewName != null)
3598     {
3599       frameTitle += viewport.viewName + " of ";
3600     }
3601
3602     frameTitle += this.title;
3603
3604     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3605   }
3606
3607   /**
3608    * DOCUMENT ME!
3609    *
3610    * @param title
3611    *          DOCUMENT ME!
3612    * @param order
3613    *          DOCUMENT ME!
3614    */
3615   public void addSortByOrderMenuItem(String title,
3616           final AlignmentOrder order)
3617   {
3618     final JMenuItem item = new JMenuItem(MessageManager
3619             .formatMessage("action.by_title_param", new Object[]
3620             { title }));
3621     sort.add(item);
3622     item.addActionListener(new java.awt.event.ActionListener()
3623     {
3624       @Override
3625       public void actionPerformed(ActionEvent e)
3626       {
3627         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3628
3629         // TODO: JBPNote - have to map order entries to curent SequenceI
3630         // pointers
3631         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3632
3633         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3634                 viewport.getAlignment()));
3635
3636         alignPanel.paintAlignment(true, false);
3637       }
3638     });
3639   }
3640
3641   /**
3642    * Add a new sort by annotation score menu item
3643    *
3644    * @param sort
3645    *          the menu to add the option to
3646    * @param scoreLabel
3647    *          the label used to retrieve scores for each sequence on the
3648    *          alignment
3649    */
3650   public void addSortByAnnotScoreMenuItem(JMenu sort,
3651           final String scoreLabel)
3652   {
3653     final JMenuItem item = new JMenuItem(scoreLabel);
3654     sort.add(item);
3655     item.addActionListener(new java.awt.event.ActionListener()
3656     {
3657       @Override
3658       public void actionPerformed(ActionEvent e)
3659       {
3660         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3661         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3662                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3663         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3664                 viewport.getAlignment()));
3665         alignPanel.paintAlignment(true, false);
3666       }
3667     });
3668   }
3669
3670   /**
3671    * last hash for alignment's annotation array - used to minimise cost of
3672    * rebuild.
3673    */
3674   protected int _annotationScoreVectorHash;
3675
3676   /**
3677    * search the alignment and rebuild the sort by annotation score submenu the
3678    * last alignment annotation vector hash is stored to minimize cost of
3679    * rebuilding in subsequence calls.
3680    *
3681    */
3682   @Override
3683   public void buildSortByAnnotationScoresMenu()
3684   {
3685     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3686     {
3687       return;
3688     }
3689
3690     if (viewport.getAlignment().getAlignmentAnnotation()
3691             .hashCode() != _annotationScoreVectorHash)
3692     {
3693       sortByAnnotScore.removeAll();
3694       // almost certainly a quicker way to do this - but we keep it simple
3695       Hashtable scoreSorts = new Hashtable();
3696       AlignmentAnnotation aann[];
3697       for (SequenceI sqa : viewport.getAlignment().getSequences())
3698       {
3699         aann = sqa.getAnnotation();
3700         for (int i = 0; aann != null && i < aann.length; i++)
3701         {
3702           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3703           {
3704             scoreSorts.put(aann[i].label, aann[i].label);
3705           }
3706         }
3707       }
3708       Enumeration labels = scoreSorts.keys();
3709       while (labels.hasMoreElements())
3710       {
3711         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3712                 (String) labels.nextElement());
3713       }
3714       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3715       scoreSorts.clear();
3716
3717       _annotationScoreVectorHash = viewport.getAlignment()
3718               .getAlignmentAnnotation().hashCode();
3719     }
3720   }
3721
3722   /**
3723    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3724    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3725    * call. Listeners are added to remove the menu item when the treePanel is
3726    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3727    * modified.
3728    */
3729   @Override
3730   public void buildTreeSortMenu()
3731   {
3732     sortByTreeMenu.removeAll();
3733
3734     List<Component> comps = PaintRefresher.components
3735             .get(viewport.getSequenceSetId());
3736     List<TreePanel> treePanels = new ArrayList<>();
3737     for (Component comp : comps)
3738     {
3739       if (comp instanceof TreePanel)
3740       {
3741         treePanels.add((TreePanel) comp);
3742       }
3743     }
3744
3745     if (treePanels.size() < 1)
3746     {
3747       sortByTreeMenu.setVisible(false);
3748       return;
3749     }
3750
3751     sortByTreeMenu.setVisible(true);
3752
3753     for (final TreePanel tp : treePanels)
3754     {
3755       final JMenuItem item = new JMenuItem(tp.getTitle());
3756       item.addActionListener(new java.awt.event.ActionListener()
3757       {
3758         @Override
3759         public void actionPerformed(ActionEvent e)
3760         {
3761           tp.sortByTree_actionPerformed();
3762           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3763
3764         }
3765       });
3766
3767       sortByTreeMenu.add(item);
3768     }
3769   }
3770
3771   public boolean sortBy(AlignmentOrder alorder, String undoname)
3772   {
3773     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3774     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3775     if (undoname != null)
3776     {
3777       addHistoryItem(new OrderCommand(undoname, oldOrder,
3778               viewport.getAlignment()));
3779     }
3780     alignPanel.paintAlignment(true, false);
3781     return true;
3782   }
3783
3784   /**
3785    * Work out whether the whole set of sequences or just the selected set will
3786    * be submitted for multiple alignment.
3787    *
3788    */
3789   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3790   {
3791     // Now, check we have enough sequences
3792     AlignmentView msa = null;
3793
3794     if ((viewport.getSelectionGroup() != null)
3795             && (viewport.getSelectionGroup().getSize() > 1))
3796     {
3797       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3798       // some common interface!
3799       /*
3800        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3801        * SequenceI[sz = seqs.getSize(false)];
3802        *
3803        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3804        * seqs.getSequenceAt(i); }
3805        */
3806       msa = viewport.getAlignmentView(true);
3807     }
3808     else if (viewport.getSelectionGroup() != null
3809             && viewport.getSelectionGroup().getSize() == 1)
3810     {
3811       int option = JvOptionPane.showConfirmDialog(this,
3812               MessageManager.getString("warn.oneseq_msainput_selection"),
3813               MessageManager.getString("label.invalid_selection"),
3814               JvOptionPane.OK_CANCEL_OPTION);
3815       if (option == JvOptionPane.OK_OPTION)
3816       {
3817         msa = viewport.getAlignmentView(false);
3818       }
3819     }
3820     else
3821     {
3822       msa = viewport.getAlignmentView(false);
3823     }
3824     return msa;
3825   }
3826
3827   /**
3828    * Decides what is submitted to a secondary structure prediction service: the
3829    * first sequence in the alignment, or in the current selection, or, if the
3830    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3831    * region or the whole alignment. (where the first sequence in the set is the
3832    * one that the prediction will be for).
3833    */
3834   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3835   {
3836     AlignmentView seqs = null;
3837
3838     if ((viewport.getSelectionGroup() != null)
3839             && (viewport.getSelectionGroup().getSize() > 0))
3840     {
3841       seqs = viewport.getAlignmentView(true);
3842     }
3843     else
3844     {
3845       seqs = viewport.getAlignmentView(false);
3846     }
3847     // limit sequences - JBPNote in future - could spawn multiple prediction
3848     // jobs
3849     // TODO: viewport.getAlignment().isAligned is a global state - the local
3850     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3851     if (!viewport.getAlignment().isAligned(false))
3852     {
3853       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3854       // TODO: if seqs.getSequences().length>1 then should really have warned
3855       // user!
3856
3857     }
3858     return seqs;
3859   }
3860
3861   /**
3862    * DOCUMENT ME!
3863    *
3864    * @param e
3865    *          DOCUMENT ME!
3866    */
3867   @Override
3868   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3869   {
3870     // Pick the tree file
3871     JalviewFileChooser chooser = new JalviewFileChooser(
3872             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3873     chooser.setFileView(new JalviewFileView());
3874     chooser.setDialogTitle(
3875             MessageManager.getString("label.select_newick_like_tree_file"));
3876     chooser.setToolTipText(
3877             MessageManager.getString("label.load_tree_file"));
3878
3879     int value = chooser.showOpenDialog(null);
3880
3881     if (value == JalviewFileChooser.APPROVE_OPTION)
3882     {
3883       String filePath = chooser.getSelectedFile().getPath();
3884       Cache.setProperty("LAST_DIRECTORY", filePath);
3885       NewickFile fin = null;
3886       try
3887       {
3888         fin = new NewickFile(filePath, DataSourceType.FILE);
3889         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3890       } catch (Exception ex)
3891       {
3892         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3893                 MessageManager.getString("label.problem_reading_tree_file"),
3894                 JvOptionPane.WARNING_MESSAGE);
3895         ex.printStackTrace();
3896       }
3897       if (fin != null && fin.hasWarningMessage())
3898       {
3899         JvOptionPane.showMessageDialog(Desktop.desktop,
3900                 fin.getWarningMessage(),
3901                 MessageManager
3902                         .getString("label.possible_problem_with_tree_file"),
3903                 JvOptionPane.WARNING_MESSAGE);
3904       }
3905     }
3906   }
3907
3908   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3909   {
3910     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3911   }
3912
3913   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3914           int h, int x, int y)
3915   {
3916     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3917   }
3918
3919   /**
3920    * Add a treeviewer for the tree extracted from a Newick file object to the
3921    * current alignment view
3922    *
3923    * @param nf
3924    *          the tree
3925    * @param title
3926    *          tree viewer title
3927    * @param input
3928    *          Associated alignment input data (or null)
3929    * @param w
3930    *          width
3931    * @param h
3932    *          height
3933    * @param x
3934    *          position
3935    * @param y
3936    *          position
3937    * @return TreePanel handle
3938    */
3939   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3940           AlignmentView input, int w, int h, int x, int y)
3941   {
3942     TreePanel tp = null;
3943
3944     try
3945     {
3946       nf.parse();
3947
3948       if (nf.getTree() != null)
3949       {
3950         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3951
3952         tp.setSize(w, h);
3953
3954         if (x > 0 && y > 0)
3955         {
3956           tp.setLocation(x, y);
3957         }
3958
3959         Desktop.addInternalFrame(tp, treeTitle, w, h);
3960       }
3961     } catch (Exception ex)
3962     {
3963       ex.printStackTrace();
3964     }
3965
3966     return tp;
3967   }
3968
3969   private boolean buildingMenu = false;
3970
3971   /**
3972    * Generates menu items and listener event actions for web service clients
3973    *
3974    */
3975   public void BuildWebServiceMenu()
3976   {
3977     while (buildingMenu)
3978     {
3979       try
3980       {
3981         System.err.println("Waiting for building menu to finish.");
3982         Thread.sleep(10);
3983       } catch (Exception e)
3984       {
3985       }
3986     }
3987     final AlignFrame me = this;
3988     buildingMenu = true;
3989     new Thread(new Runnable()
3990     {
3991       @Override
3992       public void run()
3993       {
3994         final List<JMenuItem> legacyItems = new ArrayList<>();
3995         try
3996         {
3997           // System.err.println("Building ws menu again "
3998           // + Thread.currentThread());
3999           // TODO: add support for context dependent disabling of services based
4000           // on
4001           // alignment and current selection
4002           // TODO: add additional serviceHandle parameter to specify abstract
4003           // handler
4004           // class independently of AbstractName
4005           // TODO: add in rediscovery GUI function to restart discoverer
4006           // TODO: group services by location as well as function and/or
4007           // introduce
4008           // object broker mechanism.
4009           final Vector<JMenu> wsmenu = new Vector<>();
4010           final IProgressIndicator af = me;
4011
4012           /*
4013            * do not i18n these strings - they are hard-coded in class
4014            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4015            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4016            */
4017           final JMenu msawsmenu = new JMenu("Alignment");
4018           final JMenu secstrmenu = new JMenu(
4019                   "Secondary Structure Prediction");
4020           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4021           final JMenu analymenu = new JMenu("Analysis");
4022           final JMenu dismenu = new JMenu("Protein Disorder");
4023           // JAL-940 - only show secondary structure prediction services from
4024           // the legacy server
4025           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4026               // &&
4027           Discoverer.services != null && (Discoverer.services.size() > 0))
4028           {
4029             // TODO: refactor to allow list of AbstractName/Handler bindings to
4030             // be
4031             // stored or retrieved from elsewhere
4032             // No MSAWS used any more:
4033             // Vector msaws = null; // (Vector)
4034             // Discoverer.services.get("MsaWS");
4035             Vector secstrpr = (Vector) Discoverer.services
4036                     .get("SecStrPred");
4037             if (secstrpr != null)
4038             {
4039               // Add any secondary structure prediction services
4040               for (int i = 0, j = secstrpr.size(); i < j; i++)
4041               {
4042                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4043                         .get(i);
4044                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4045                         .getServiceClient(sh);
4046                 int p = secstrmenu.getItemCount();
4047                 impl.attachWSMenuEntry(secstrmenu, me);
4048                 int q = secstrmenu.getItemCount();
4049                 for (int litm = p; litm < q; litm++)
4050                 {
4051                   legacyItems.add(secstrmenu.getItem(litm));
4052                 }
4053               }
4054             }
4055           }
4056
4057           // Add all submenus in the order they should appear on the web
4058           // services menu
4059           wsmenu.add(msawsmenu);
4060           wsmenu.add(secstrmenu);
4061           wsmenu.add(dismenu);
4062           wsmenu.add(analymenu);
4063           // No search services yet
4064           // wsmenu.add(seqsrchmenu);
4065
4066           javax.swing.SwingUtilities.invokeLater(new Runnable()
4067           {
4068             @Override
4069             public void run()
4070             {
4071               try
4072               {
4073                 webService.removeAll();
4074                 // first, add discovered services onto the webservices menu
4075                 if (wsmenu.size() > 0)
4076                 {
4077                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4078                   {
4079                     webService.add(wsmenu.get(i));
4080                   }
4081                 }
4082                 else
4083                 {
4084                   webService.add(me.webServiceNoServices);
4085                 }
4086                 // TODO: move into separate menu builder class.
4087                 boolean new_sspred = false;
4088                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4089                 {
4090                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4091                   if (jws2servs != null)
4092                   {
4093                     if (jws2servs.hasServices())
4094                     {
4095                       jws2servs.attachWSMenuEntry(webService, me);
4096                       for (Jws2Instance sv : jws2servs.getServices())
4097                       {
4098                         if (sv.description.toLowerCase().contains("jpred"))
4099                         {
4100                           for (JMenuItem jmi : legacyItems)
4101                           {
4102                             jmi.setVisible(false);
4103                           }
4104                         }
4105                       }
4106
4107                     }
4108                     if (jws2servs.isRunning())
4109                     {
4110                       JMenuItem tm = new JMenuItem(
4111                               "Still discovering JABA Services");
4112                       tm.setEnabled(false);
4113                       webService.add(tm);
4114                     }
4115                   }
4116                 }
4117                 build_urlServiceMenu(me.webService);
4118                 build_fetchdbmenu(webService);
4119                 for (JMenu item : wsmenu)
4120                 {
4121                   if (item.getItemCount() == 0)
4122                   {
4123                     item.setEnabled(false);
4124                   }
4125                   else
4126                   {
4127                     item.setEnabled(true);
4128                   }
4129                 }
4130               } catch (Exception e)
4131               {
4132                 Cache.log.debug(
4133                         "Exception during web service menu building process.",
4134                         e);
4135               }
4136             }
4137           });
4138         } catch (Exception e)
4139         {
4140         }
4141         buildingMenu = false;
4142       }
4143     }).start();
4144
4145   }
4146
4147   /**
4148    * construct any groupURL type service menu entries.
4149    *
4150    * @param webService
4151    */
4152   private void build_urlServiceMenu(JMenu webService)
4153   {
4154     // TODO: remove this code when 2.7 is released
4155     // DEBUG - alignmentView
4156     /*
4157      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4158      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4159      *
4160      * @Override public void actionPerformed(ActionEvent e) {
4161      * jalview.datamodel.AlignmentView
4162      * .testSelectionViews(af.viewport.getAlignment(),
4163      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4164      *
4165      * }); webService.add(testAlView);
4166      */
4167     // TODO: refactor to RestClient discoverer and merge menu entries for
4168     // rest-style services with other types of analysis/calculation service
4169     // SHmmr test client - still being implemented.
4170     // DEBUG - alignmentView
4171
4172     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4173             .getRestClients())
4174     {
4175       client.attachWSMenuEntry(
4176               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4177               this);
4178     }
4179   }
4180
4181   /**
4182    * Searches the alignment sequences for xRefs and builds the Show
4183    * Cross-References menu (formerly called Show Products), with database
4184    * sources for which cross-references are found (protein sources for a
4185    * nucleotide alignment and vice versa)
4186    *
4187    * @return true if Show Cross-references menu should be enabled
4188    */
4189   public boolean canShowProducts()
4190   {
4191     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4192     AlignmentI dataset = viewport.getAlignment().getDataset();
4193
4194     showProducts.removeAll();
4195     final boolean dna = viewport.getAlignment().isNucleotide();
4196
4197     if (seqs == null || seqs.length == 0)
4198     {
4199       // nothing to see here.
4200       return false;
4201     }
4202
4203     boolean showp = false;
4204     try
4205     {
4206       List<String> ptypes = new CrossRef(seqs, dataset)
4207               .findXrefSourcesForSequences(dna);
4208
4209       for (final String source : ptypes)
4210       {
4211         showp = true;
4212         final AlignFrame af = this;
4213         JMenuItem xtype = new JMenuItem(source);
4214         xtype.addActionListener(new ActionListener()
4215         {
4216           @Override
4217           public void actionPerformed(ActionEvent e)
4218           {
4219             showProductsFor(af.viewport.getSequenceSelection(), dna,
4220                     source);
4221           }
4222         });
4223         showProducts.add(xtype);
4224       }
4225       showProducts.setVisible(showp);
4226       showProducts.setEnabled(showp);
4227     } catch (Exception e)
4228     {
4229       Cache.log.warn(
4230               "canShowProducts threw an exception - please report to help@jalview.org",
4231               e);
4232       return false;
4233     }
4234     return showp;
4235   }
4236
4237   /**
4238    * Finds and displays cross-references for the selected sequences (protein
4239    * products for nucleotide sequences, dna coding sequences for peptides).
4240    *
4241    * @param sel
4242    *          the sequences to show cross-references for
4243    * @param dna
4244    *          true if from a nucleotide alignment (so showing proteins)
4245    * @param source
4246    *          the database to show cross-references for
4247    */
4248   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4249           final String source)
4250   {
4251     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4252             .start();
4253   }
4254
4255   /**
4256    * Construct and display a new frame containing the translation of this
4257    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4258    */
4259   @Override
4260   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4261   {
4262     AlignmentI al = null;
4263     try
4264     {
4265       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4266
4267       al = dna.translateCdna(codeTable);
4268     } catch (Exception ex)
4269     {
4270       jalview.bin.Cache.log.error(
4271               "Exception during translation. Please report this !", ex);
4272       final String msg = MessageManager.getString(
4273               "label.error_when_translating_sequences_submit_bug_report");
4274       final String errorTitle = MessageManager
4275               .getString("label.implementation_error")
4276               + MessageManager.getString("label.translation_failed");
4277       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4278               JvOptionPane.ERROR_MESSAGE);
4279       return;
4280     }
4281     if (al == null || al.getHeight() == 0)
4282     {
4283       final String msg = MessageManager.getString(
4284               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4285       final String errorTitle = MessageManager
4286               .getString("label.translation_failed");
4287       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4288               JvOptionPane.WARNING_MESSAGE);
4289     }
4290     else
4291     {
4292       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4293       af.setFileFormat(this.currentFileFormat);
4294       final String newTitle = MessageManager
4295               .formatMessage("label.translation_of_params", new Object[]
4296               { this.getTitle(), codeTable.getId() });
4297       af.setTitle(newTitle);
4298       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4299       {
4300         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4301         viewport.openSplitFrame(af, new Alignment(seqs));
4302       }
4303       else
4304       {
4305         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4306                 DEFAULT_HEIGHT);
4307       }
4308     }
4309   }
4310
4311   /**
4312    * Set the file format
4313    *
4314    * @param format
4315    */
4316   public void setFileFormat(FileFormatI format)
4317   {
4318     this.currentFileFormat = format;
4319   }
4320
4321   /**
4322    * Try to load a features file onto the alignment.
4323    *
4324    * @param file
4325    *          contents or path to retrieve file
4326    * @param sourceType
4327    *          access mode of file (see jalview.io.AlignFile)
4328    * @return true if features file was parsed correctly.
4329    */
4330   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4331   {
4332     return avc.parseFeaturesFile(file, sourceType,
4333             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4334
4335   }
4336
4337   @Override
4338   public void refreshFeatureUI(boolean enableIfNecessary)
4339   {
4340     // note - currently this is only still here rather than in the controller
4341     // because of the featureSettings hard reference that is yet to be
4342     // abstracted
4343     if (enableIfNecessary)
4344     {
4345       viewport.setShowSequenceFeatures(true);
4346       showSeqFeatures.setSelected(true);
4347     }
4348
4349   }
4350
4351   @Override
4352   public void dragEnter(DropTargetDragEvent evt)
4353   {
4354   }
4355
4356   @Override
4357   public void dragExit(DropTargetEvent evt)
4358   {
4359   }
4360
4361   @Override
4362   public void dragOver(DropTargetDragEvent evt)
4363   {
4364   }
4365
4366   @Override
4367   public void dropActionChanged(DropTargetDragEvent evt)
4368   {
4369   }
4370
4371   @Override
4372   public void drop(DropTargetDropEvent evt)
4373   {
4374     // JAL-1552 - acceptDrop required before getTransferable call for
4375     // Java's Transferable for native dnd
4376     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4377     Transferable t = evt.getTransferable();
4378     final AlignFrame thisaf = this;
4379     final List<String> files = new ArrayList<>();
4380     List<DataSourceType> protocols = new ArrayList<>();
4381
4382     try
4383     {
4384       Desktop.transferFromDropTarget(files, protocols, evt, t);
4385     } catch (Exception e)
4386     {
4387       e.printStackTrace();
4388     }
4389     if (files != null)
4390     {
4391       new Thread(new Runnable()
4392       {
4393         @Override
4394         public void run()
4395         {
4396           try
4397           {
4398             // check to see if any of these files have names matching sequences
4399             // in
4400             // the alignment
4401             SequenceIdMatcher idm = new SequenceIdMatcher(
4402                     viewport.getAlignment().getSequencesArray());
4403             /**
4404              * Object[] { String,SequenceI}
4405              */
4406             ArrayList<Object[]> filesmatched = new ArrayList<>();
4407             ArrayList<String> filesnotmatched = new ArrayList<>();
4408             for (int i = 0; i < files.size(); i++)
4409             {
4410               String file = files.get(i).toString();
4411               String pdbfn = "";
4412               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4413               if (protocol == DataSourceType.FILE)
4414               {
4415                 File fl = new File(file);
4416                 pdbfn = fl.getName();
4417               }
4418               else if (protocol == DataSourceType.URL)
4419               {
4420                 URL url = new URL(file);
4421                 pdbfn = url.getFile();
4422               }
4423               if (pdbfn.length() > 0)
4424               {
4425                 // attempt to find a match in the alignment
4426                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4427                 int l = 0, c = pdbfn.indexOf(".");
4428                 while (mtch == null && c != -1)
4429                 {
4430                   do
4431                   {
4432                     l = c;
4433                   } while ((c = pdbfn.indexOf(".", l)) > l);
4434                   if (l > -1)
4435                   {
4436                     pdbfn = pdbfn.substring(0, l);
4437                   }
4438                   mtch = idm.findAllIdMatches(pdbfn);
4439                 }
4440                 if (mtch != null)
4441                 {
4442                   FileFormatI type = null;
4443                   try
4444                   {
4445                     type = new IdentifyFile().identify(file, protocol);
4446                   } catch (Exception ex)
4447                   {
4448                     type = null;
4449                   }
4450                   if (type != null && type.isStructureFile())
4451                   {
4452                     filesmatched.add(new Object[] { file, protocol, mtch });
4453                     continue;
4454                   }
4455                 }
4456                 // File wasn't named like one of the sequences or wasn't a PDB
4457                 // file.
4458                 filesnotmatched.add(file);
4459               }
4460             }
4461             int assocfiles = 0;
4462             if (filesmatched.size() > 0)
4463             {
4464               if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4465                       || JvOptionPane.showConfirmDialog(thisaf,
4466                               MessageManager.formatMessage(
4467                                       "label.automatically_associate_structure_files_with_sequences_same_name",
4468                                       new Object[]
4469                                       { Integer.valueOf(filesmatched.size())
4470                                               .toString() }),
4471                               MessageManager.getString(
4472                                       "label.automatically_associate_structure_files_by_name"),
4473                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4474
4475               {
4476                 for (Object[] fm : filesmatched)
4477                 {
4478                   // try and associate
4479                   // TODO: may want to set a standard ID naming formalism for
4480                   // associating PDB files which have no IDs.
4481                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4482                   {
4483                     PDBEntry pe = new AssociatePdbFileWithSeq()
4484                             .associatePdbWithSeq((String) fm[0],
4485                                     (DataSourceType) fm[1], toassoc, false,
4486                                     Desktop.instance);
4487                     if (pe != null)
4488                     {
4489                       System.err.println("Associated file : "
4490                               + ((String) fm[0]) + " with "
4491                               + toassoc.getDisplayId(true));
4492                       assocfiles++;
4493                     }
4494                   }
4495                   // TODO: do we need to update overview ? only if features are
4496                   // shown I guess
4497                   alignPanel.paintAlignment(true, false);
4498                 }
4499               }
4500             }
4501             if (filesnotmatched.size() > 0)
4502             {
4503               if (assocfiles > 0 && (Cache.getDefault(
4504                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4505                       || JvOptionPane.showConfirmDialog(thisaf,
4506                               "<html>" + MessageManager.formatMessage(
4507                                       "label.ignore_unmatched_dropped_files_info",
4508                                       new Object[]
4509                                       { Integer.valueOf(
4510                                               filesnotmatched.size())
4511                                               .toString() })
4512                                       + "</html>",
4513                               MessageManager.getString(
4514                                       "label.ignore_unmatched_dropped_files"),
4515                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4516               {
4517                 return;
4518               }
4519               for (String fn : filesnotmatched)
4520               {
4521                 loadJalviewDataFile(fn, null, null, null);
4522               }
4523
4524             }
4525           } catch (Exception ex)
4526           {
4527             ex.printStackTrace();
4528           }
4529         }
4530       }).start();
4531     }
4532   }
4533
4534   /**
4535    * Attempt to load a "dropped" file or URL string, by testing in turn for
4536    * <ul>
4537    * <li>an Annotation file</li>
4538    * <li>a JNet file</li>
4539    * <li>a features file</li>
4540    * <li>else try to interpret as an alignment file</li>
4541    * </ul>
4542    *
4543    * @param file
4544    *          either a filename or a URL string.
4545    */
4546   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4547           FileFormatI format, SequenceI assocSeq)
4548   {
4549     try
4550     {
4551       if (sourceType == null)
4552       {
4553         sourceType = FormatAdapter.checkProtocol(file);
4554       }
4555       // if the file isn't identified, or not positively identified as some
4556       // other filetype (PFAM is default unidentified alignment file type) then
4557       // try to parse as annotation.
4558       boolean isAnnotation = (format == null
4559               || FileFormat.Pfam.equals(format))
4560                       ? new AnnotationFile().annotateAlignmentView(viewport,
4561                               file, sourceType)
4562                       : false;
4563
4564       if (!isAnnotation)
4565       {
4566         // first see if its a T-COFFEE score file
4567         TCoffeeScoreFile tcf = null;
4568         try
4569         {
4570           tcf = new TCoffeeScoreFile(file, sourceType);
4571           if (tcf.isValid())
4572           {
4573             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4574             {
4575               buildColourMenu();
4576               changeColour(
4577                       new TCoffeeColourScheme(viewport.getAlignment()));
4578               isAnnotation = true;
4579               statusBar.setText(MessageManager.getString(
4580                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4581             }
4582             else
4583             {
4584               // some problem - if no warning its probable that the ID matching
4585               // process didn't work
4586               JvOptionPane.showMessageDialog(Desktop.desktop,
4587                       tcf.getWarningMessage() == null
4588                               ? MessageManager.getString(
4589                                       "label.check_file_matches_sequence_ids_alignment")
4590                               : tcf.getWarningMessage(),
4591                       MessageManager.getString(
4592                               "label.problem_reading_tcoffee_score_file"),
4593                       JvOptionPane.WARNING_MESSAGE);
4594             }
4595           }
4596           else
4597           {
4598             tcf = null;
4599           }
4600         } catch (Exception x)
4601         {
4602           Cache.log.debug(
4603                   "Exception when processing data source as T-COFFEE score file",
4604                   x);
4605           tcf = null;
4606         }
4607         if (tcf == null)
4608         {
4609           // try to see if its a JNet 'concise' style annotation file *before*
4610           // we
4611           // try to parse it as a features file
4612           if (format == null)
4613           {
4614             format = new IdentifyFile().identify(file, sourceType);
4615           }
4616           if (FileFormat.ScoreMatrix == format)
4617           {
4618             ScoreMatrixFile sm = new ScoreMatrixFile(
4619                     new FileParse(file, sourceType));
4620             sm.parse();
4621             // todo: i18n this message
4622             statusBar.setText(MessageManager.formatMessage(
4623                     "label.successfully_loaded_matrix",
4624                     sm.getMatrixName()));
4625           }
4626           else if (FileFormat.Jnet.equals(format))
4627           {
4628             JPredFile predictions = new JPredFile(file, sourceType);
4629             new JnetAnnotationMaker();
4630             JnetAnnotationMaker.add_annotation(predictions,
4631                     viewport.getAlignment(), 0, false);
4632             viewport.getAlignment().setupJPredAlignment();
4633             isAnnotation = true;
4634           }
4635           // else if (IdentifyFile.FeaturesFile.equals(format))
4636           else if (FileFormat.Features.equals(format))
4637           {
4638             if (parseFeaturesFile(file, sourceType))
4639             {
4640               alignPanel.paintAlignment(true, true);
4641             }
4642           }
4643           else
4644           {
4645             new FileLoader().LoadFile(viewport, file, sourceType, format);
4646           }
4647         }
4648       }
4649       if (isAnnotation)
4650       {
4651
4652         alignPanel.adjustAnnotationHeight();
4653         viewport.updateSequenceIdColours();
4654         buildSortByAnnotationScoresMenu();
4655         alignPanel.paintAlignment(true, true);
4656       }
4657     } catch (Exception ex)
4658     {
4659       ex.printStackTrace();
4660     } catch (OutOfMemoryError oom)
4661     {
4662       try
4663       {
4664         System.gc();
4665       } catch (Exception x)
4666       {
4667       }
4668       new OOMWarning(
4669               "loading data "
4670                       + (sourceType != null
4671                               ? (sourceType == DataSourceType.PASTE
4672                                       ? "from clipboard."
4673                                       : "using " + sourceType + " from "
4674                                               + file)
4675                               : ".")
4676                       + (format != null
4677                               ? "(parsing as '" + format + "' file)"
4678                               : ""),
4679               oom, Desktop.desktop);
4680     }
4681   }
4682
4683   /**
4684    * Method invoked by the ChangeListener on the tabbed pane, in other words
4685    * when a different tabbed pane is selected by the user or programmatically.
4686    */
4687   @Override
4688   public void tabSelectionChanged(int index)
4689   {
4690     if (index > -1)
4691     {
4692       alignPanel = alignPanels.get(index);
4693       viewport = alignPanel.av;
4694       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4695       setMenusFromViewport(viewport);
4696     }
4697
4698     /*
4699      * 'focus' any colour slider that is open to the selected viewport
4700      */
4701     if (viewport.getConservationSelected())
4702     {
4703       SliderPanel.setConservationSlider(alignPanel,
4704               viewport.getResidueShading(), alignPanel.getViewName());
4705     }
4706     else
4707     {
4708       SliderPanel.hideConservationSlider();
4709     }
4710     if (viewport.getAbovePIDThreshold())
4711     {
4712       SliderPanel.setPIDSliderSource(alignPanel,
4713               viewport.getResidueShading(), alignPanel.getViewName());
4714     }
4715     else
4716     {
4717       SliderPanel.hidePIDSlider();
4718     }
4719
4720     /*
4721      * If there is a frame linked to this one in a SplitPane, switch it to the
4722      * same view tab index. No infinite recursion of calls should happen, since
4723      * tabSelectionChanged() should not get invoked on setting the selected
4724      * index to an unchanged value. Guard against setting an invalid index
4725      * before the new view peer tab has been created.
4726      */
4727     final AlignViewportI peer = viewport.getCodingComplement();
4728     if (peer != null)
4729     {
4730       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4731               .getAlignPanel().alignFrame;
4732       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4733       {
4734         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4735       }
4736     }
4737   }
4738
4739   /**
4740    * On right mouse click on view tab, prompt for and set new view name.
4741    */
4742   @Override
4743   public void tabbedPane_mousePressed(MouseEvent e)
4744   {
4745     if (e.isPopupTrigger())
4746     {
4747       String msg = MessageManager.getString("label.enter_view_name");
4748       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4749               JvOptionPane.QUESTION_MESSAGE);
4750
4751       if (reply != null)
4752       {
4753         viewport.viewName = reply;
4754         // TODO warn if reply is in getExistingViewNames()?
4755         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4756       }
4757     }
4758   }
4759
4760   public AlignViewport getCurrentView()
4761   {
4762     return viewport;
4763   }
4764
4765   /**
4766    * Open the dialog for regex description parsing.
4767    */
4768   @Override
4769   protected void extractScores_actionPerformed(ActionEvent e)
4770   {
4771     ParseProperties pp = new jalview.analysis.ParseProperties(
4772             viewport.getAlignment());
4773     // TODO: verify regex and introduce GUI dialog for version 2.5
4774     // if (pp.getScoresFromDescription("col", "score column ",
4775     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4776     // true)>0)
4777     if (pp.getScoresFromDescription("description column",
4778             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4779     {
4780       buildSortByAnnotationScoresMenu();
4781     }
4782   }
4783
4784   /*
4785    * (non-Javadoc)
4786    *
4787    * @see
4788    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4789    * )
4790    */
4791   @Override
4792   protected void showDbRefs_actionPerformed(ActionEvent e)
4793   {
4794     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4795   }
4796
4797   /*
4798    * (non-Javadoc)
4799    *
4800    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4801    * ActionEvent)
4802    */
4803   @Override
4804   protected void showNpFeats_actionPerformed(ActionEvent e)
4805   {
4806     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4807   }
4808
4809   /**
4810    * find the viewport amongst the tabs in this alignment frame and close that
4811    * tab
4812    *
4813    * @param av
4814    */
4815   public boolean closeView(AlignViewportI av)
4816   {
4817     if (viewport == av)
4818     {
4819       this.closeMenuItem_actionPerformed(false);
4820       return true;
4821     }
4822     Component[] comp = tabbedPane.getComponents();
4823     for (int i = 0; comp != null && i < comp.length; i++)
4824     {
4825       if (comp[i] instanceof AlignmentPanel)
4826       {
4827         if (((AlignmentPanel) comp[i]).av == av)
4828         {
4829           // close the view.
4830           closeView((AlignmentPanel) comp[i]);
4831           return true;
4832         }
4833       }
4834     }
4835     return false;
4836   }
4837
4838   protected void build_fetchdbmenu(JMenu webService)
4839   {
4840     // Temporary hack - DBRef Fetcher always top level ws entry.
4841     // TODO We probably want to store a sequence database checklist in
4842     // preferences and have checkboxes.. rather than individual sources selected
4843     // here
4844     final JMenu rfetch = new JMenu(
4845             MessageManager.getString("action.fetch_db_references"));
4846     rfetch.setToolTipText(MessageManager.getString(
4847             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4848     webService.add(rfetch);
4849
4850     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4851             MessageManager.getString("option.trim_retrieved_seqs"));
4852     trimrs.setToolTipText(
4853             MessageManager.getString("label.trim_retrieved_sequences"));
4854     trimrs.setSelected(
4855             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4856     trimrs.addActionListener(new ActionListener()
4857     {
4858       @Override
4859       public void actionPerformed(ActionEvent e)
4860       {
4861         trimrs.setSelected(trimrs.isSelected());
4862         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4863                 Boolean.valueOf(trimrs.isSelected()).toString());
4864       };
4865     });
4866     rfetch.add(trimrs);
4867     JMenuItem fetchr = new JMenuItem(
4868             MessageManager.getString("label.standard_databases"));
4869     fetchr.setToolTipText(
4870             MessageManager.getString("label.fetch_embl_uniprot"));
4871     fetchr.addActionListener(new ActionListener()
4872     {
4873
4874       @Override
4875       public void actionPerformed(ActionEvent e)
4876       {
4877         new Thread(new Runnable()
4878         {
4879           @Override
4880           public void run()
4881           {
4882             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4883                     .getAlignment().isNucleotide();
4884             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4885                     alignPanel.av.getSequenceSelection(),
4886                     alignPanel.alignFrame, null,
4887                     alignPanel.alignFrame.featureSettings, isNucleotide);
4888             dbRefFetcher.addListener(new FetchFinishedListenerI()
4889             {
4890               @Override
4891               public void finished()
4892               {
4893                 AlignFrame.this.setMenusForViewport();
4894               }
4895             });
4896             dbRefFetcher.fetchDBRefs(false);
4897           }
4898         }).start();
4899
4900       }
4901
4902     });
4903     rfetch.add(fetchr);
4904     final AlignFrame me = this;
4905     new Thread(new Runnable()
4906     {
4907       @Override
4908       public void run()
4909       {
4910         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4911                 .getSequenceFetcherSingleton(me);
4912         javax.swing.SwingUtilities.invokeLater(new Runnable()
4913         {
4914           @Override
4915           public void run()
4916           {
4917             String[] dbclasses = sf.getOrderedSupportedSources();
4918             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4919             // jalview.util.QuickSort.sort(otherdb, otherdb);
4920             List<DbSourceProxy> otherdb;
4921             JMenu dfetch = new JMenu();
4922             JMenu ifetch = new JMenu();
4923             JMenuItem fetchr = null;
4924             int comp = 0, icomp = 0, mcomp = 15;
4925             String mname = null;
4926             int dbi = 0;
4927             for (String dbclass : dbclasses)
4928             {
4929               otherdb = sf.getSourceProxy(dbclass);
4930               // add a single entry for this class, or submenu allowing 'fetch
4931               // all' or pick one
4932               if (otherdb == null || otherdb.size() < 1)
4933               {
4934                 continue;
4935               }
4936               // List<DbSourceProxy> dbs=otherdb;
4937               // otherdb=new ArrayList<DbSourceProxy>();
4938               // for (DbSourceProxy db:dbs)
4939               // {
4940               // if (!db.isA(DBRefSource.ALIGNMENTDB)
4941               // }
4942               if (mname == null)
4943               {
4944                 mname = "From " + dbclass;
4945               }
4946               if (otherdb.size() == 1)
4947               {
4948                 final DbSourceProxy[] dassource = otherdb
4949                         .toArray(new DbSourceProxy[0]);
4950                 DbSourceProxy src = otherdb.get(0);
4951                 fetchr = new JMenuItem(src.getDbSource());
4952                 fetchr.addActionListener(new ActionListener()
4953                 {
4954
4955                   @Override
4956                   public void actionPerformed(ActionEvent e)
4957                   {
4958                     new Thread(new Runnable()
4959                     {
4960
4961                       @Override
4962                       public void run()
4963                       {
4964                         boolean isNucleotide = alignPanel.alignFrame
4965                                 .getViewport().getAlignment()
4966                                 .isNucleotide();
4967                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
4968                                 alignPanel.av.getSequenceSelection(),
4969                                 alignPanel.alignFrame, dassource,
4970                                 alignPanel.alignFrame.featureSettings,
4971                                 isNucleotide);
4972                         dbRefFetcher
4973                                 .addListener(new FetchFinishedListenerI()
4974                                 {
4975                                   @Override
4976                                   public void finished()
4977                                   {
4978                                     AlignFrame.this.setMenusForViewport();
4979                                   }
4980                                 });
4981                         dbRefFetcher.fetchDBRefs(false);
4982                       }
4983                     }).start();
4984                   }
4985
4986                 });
4987                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
4988                         MessageManager.formatMessage(
4989                                 "label.fetch_retrieve_from", new Object[]
4990                                 { src.getDbName() })));
4991                 dfetch.add(fetchr);
4992                 comp++;
4993               }
4994               else
4995               {
4996                 final DbSourceProxy[] dassource = otherdb
4997                         .toArray(new DbSourceProxy[0]);
4998                 // fetch all entry
4999                 DbSourceProxy src = otherdb.get(0);
5000                 fetchr = new JMenuItem(MessageManager
5001                         .formatMessage("label.fetch_all_param", new Object[]
5002                         { src.getDbSource() }));
5003                 fetchr.addActionListener(new ActionListener()
5004                 {
5005                   @Override
5006                   public void actionPerformed(ActionEvent e)
5007                   {
5008                     new Thread(new Runnable()
5009                     {
5010
5011                       @Override
5012                       public void run()
5013                       {
5014                         boolean isNucleotide = alignPanel.alignFrame
5015                                 .getViewport().getAlignment()
5016                                 .isNucleotide();
5017                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5018                                 alignPanel.av.getSequenceSelection(),
5019                                 alignPanel.alignFrame, dassource,
5020                                 alignPanel.alignFrame.featureSettings,
5021                                 isNucleotide);
5022                         dbRefFetcher
5023                                 .addListener(new FetchFinishedListenerI()
5024                                 {
5025                                   @Override
5026                                   public void finished()
5027                                   {
5028                                     AlignFrame.this.setMenusForViewport();
5029                                   }
5030                                 });
5031                         dbRefFetcher.fetchDBRefs(false);
5032                       }
5033                     }).start();
5034                   }
5035                 });
5036
5037                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5038                         MessageManager.formatMessage(
5039                                 "label.fetch_retrieve_from_all_sources",
5040                                 new Object[]
5041                                 { Integer.valueOf(otherdb.size())
5042                                         .toString(),
5043                                     src.getDbSource(), src.getDbName() })));
5044                 dfetch.add(fetchr);
5045                 comp++;
5046                 // and then build the rest of the individual menus
5047                 ifetch = new JMenu(MessageManager.formatMessage(
5048                         "label.source_from_db_source", new Object[]
5049                         { src.getDbSource() }));
5050                 icomp = 0;
5051                 String imname = null;
5052                 int i = 0;
5053                 for (DbSourceProxy sproxy : otherdb)
5054                 {
5055                   String dbname = sproxy.getDbName();
5056                   String sname = dbname.length() > 5
5057                           ? dbname.substring(0, 5) + "..."
5058                           : dbname;
5059                   String msname = dbname.length() > 10
5060                           ? dbname.substring(0, 10) + "..."
5061                           : dbname;
5062                   if (imname == null)
5063                   {
5064                     imname = MessageManager
5065                             .formatMessage("label.from_msname", new Object[]
5066                             { sname });
5067                   }
5068                   fetchr = new JMenuItem(msname);
5069                   final DbSourceProxy[] dassrc = { sproxy };
5070                   fetchr.addActionListener(new ActionListener()
5071                   {
5072
5073                     @Override
5074                     public void actionPerformed(ActionEvent e)
5075                     {
5076                       new Thread(new Runnable()
5077                       {
5078
5079                         @Override
5080                         public void run()
5081                         {
5082                           boolean isNucleotide = alignPanel.alignFrame
5083                                   .getViewport().getAlignment()
5084                                   .isNucleotide();
5085                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5086                                   alignPanel.av.getSequenceSelection(),
5087                                   alignPanel.alignFrame, dassrc,
5088                                   alignPanel.alignFrame.featureSettings,
5089                                   isNucleotide);
5090                           dbRefFetcher
5091                                   .addListener(new FetchFinishedListenerI()
5092                                   {
5093                                     @Override
5094                                     public void finished()
5095                                     {
5096                                       AlignFrame.this.setMenusForViewport();
5097                                     }
5098                                   });
5099                           dbRefFetcher.fetchDBRefs(false);
5100                         }
5101                       }).start();
5102                     }
5103
5104                   });
5105                   fetchr.setToolTipText(
5106                           "<html>" + MessageManager.formatMessage(
5107                                   "label.fetch_retrieve_from", new Object[]
5108                                   { dbname }));
5109                   ifetch.add(fetchr);
5110                   ++i;
5111                   if (++icomp >= mcomp || i == (otherdb.size()))
5112                   {
5113                     ifetch.setText(MessageManager.formatMessage(
5114                             "label.source_to_target", imname, sname));
5115                     dfetch.add(ifetch);
5116                     ifetch = new JMenu();
5117                     imname = null;
5118                     icomp = 0;
5119                     comp++;
5120                   }
5121                 }
5122               }
5123               ++dbi;
5124               if (comp >= mcomp || dbi >= (dbclasses.length))
5125               {
5126                 dfetch.setText(MessageManager.formatMessage(
5127                         "label.source_to_target", mname, dbclass));
5128                 rfetch.add(dfetch);
5129                 dfetch = new JMenu();
5130                 mname = null;
5131                 comp = 0;
5132               }
5133             }
5134           }
5135         });
5136       }
5137     }).start();
5138
5139   }
5140
5141   /**
5142    * Left justify the whole alignment.
5143    */
5144   @Override
5145   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5146   {
5147     AlignmentI al = viewport.getAlignment();
5148     al.justify(false);
5149     viewport.firePropertyChange("alignment", null, al);
5150   }
5151
5152   /**
5153    * Right justify the whole alignment.
5154    */
5155   @Override
5156   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5157   {
5158     AlignmentI al = viewport.getAlignment();
5159     al.justify(true);
5160     viewport.firePropertyChange("alignment", null, al);
5161   }
5162
5163   @Override
5164   public void setShowSeqFeatures(boolean b)
5165   {
5166     showSeqFeatures.setSelected(b);
5167     viewport.setShowSequenceFeatures(b);
5168   }
5169
5170   /*
5171    * (non-Javadoc)
5172    *
5173    * @see
5174    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5175    * awt.event.ActionEvent)
5176    */
5177   @Override
5178   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5179   {
5180     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5181     alignPanel.paintAlignment(false, false);
5182   }
5183
5184   /*
5185    * (non-Javadoc)
5186    *
5187    * @see
5188    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5189    * .ActionEvent)
5190    */
5191   @Override
5192   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5193   {
5194     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5195     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5196
5197   }
5198
5199   /*
5200    * (non-Javadoc)
5201    *
5202    * @see
5203    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5204    * .event.ActionEvent)
5205    */
5206   @Override
5207   protected void showGroupConservation_actionPerformed(ActionEvent e)
5208   {
5209     viewport.setShowGroupConservation(showGroupConservation.getState());
5210     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5211   }
5212
5213   /*
5214    * (non-Javadoc)
5215    *
5216    * @see
5217    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5218    * .event.ActionEvent)
5219    */
5220   @Override
5221   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5222   {
5223     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5224     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5225   }
5226
5227   /*
5228    * (non-Javadoc)
5229    *
5230    * @see
5231    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5232    * .event.ActionEvent)
5233    */
5234   @Override
5235   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5236   {
5237     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5238     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5239   }
5240
5241   @Override
5242   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5243   {
5244     showSequenceLogo.setState(true);
5245     viewport.setShowSequenceLogo(true);
5246     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5247     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5248   }
5249
5250   @Override
5251   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5252   {
5253     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5254   }
5255
5256   /*
5257    * (non-Javadoc)
5258    *
5259    * @see
5260    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5261    * .event.ActionEvent)
5262    */
5263   @Override
5264   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5265   {
5266     if (avc.makeGroupsFromSelection())
5267     {
5268       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5269       alignPanel.updateAnnotation();
5270       alignPanel.paintAlignment(true, true);
5271     }
5272   }
5273
5274   public void clearAlignmentSeqRep()
5275   {
5276     // TODO refactor alignmentseqrep to controller
5277     if (viewport.getAlignment().hasSeqrep())
5278     {
5279       viewport.getAlignment().setSeqrep(null);
5280       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5281       alignPanel.updateAnnotation();
5282       alignPanel.paintAlignment(true, true);
5283     }
5284   }
5285
5286   @Override
5287   protected void createGroup_actionPerformed(ActionEvent e)
5288   {
5289     if (avc.createGroup())
5290     {
5291       alignPanel.alignmentChanged();
5292     }
5293   }
5294
5295   @Override
5296   protected void unGroup_actionPerformed(ActionEvent e)
5297   {
5298     if (avc.unGroup())
5299     {
5300       alignPanel.alignmentChanged();
5301     }
5302   }
5303
5304   /**
5305    * make the given alignmentPanel the currently selected tab
5306    *
5307    * @param alignmentPanel
5308    */
5309   public void setDisplayedView(AlignmentPanel alignmentPanel)
5310   {
5311     if (!viewport.getSequenceSetId()
5312             .equals(alignmentPanel.av.getSequenceSetId()))
5313     {
5314       throw new Error(MessageManager.getString(
5315               "error.implementation_error_cannot_show_view_alignment_frame"));
5316     }
5317     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5318             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5319     {
5320       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5321     }
5322   }
5323
5324   /**
5325    * Action on selection of menu options to Show or Hide annotations.
5326    *
5327    * @param visible
5328    * @param forSequences
5329    *          update sequence-related annotations
5330    * @param forAlignment
5331    *          update non-sequence-related annotations
5332    */
5333   @Override
5334   protected void setAnnotationsVisibility(boolean visible,
5335           boolean forSequences, boolean forAlignment)
5336   {
5337     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5338             .getAlignmentAnnotation();
5339     if (anns == null)
5340     {
5341       return;
5342     }
5343     for (AlignmentAnnotation aa : anns)
5344     {
5345       /*
5346        * don't display non-positional annotations on an alignment
5347        */
5348       if (aa.annotations == null)
5349       {
5350         continue;
5351       }
5352       boolean apply = (aa.sequenceRef == null && forAlignment)
5353               || (aa.sequenceRef != null && forSequences);
5354       if (apply)
5355       {
5356         aa.visible = visible;
5357       }
5358     }
5359     alignPanel.validateAnnotationDimensions(true);
5360     alignPanel.alignmentChanged();
5361   }
5362
5363   /**
5364    * Store selected annotation sort order for the view and repaint.
5365    */
5366   @Override
5367   protected void sortAnnotations_actionPerformed()
5368   {
5369     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5370     this.alignPanel.av
5371             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5372     alignPanel.paintAlignment(false, false);
5373   }
5374
5375   /**
5376    *
5377    * @return alignment panels in this alignment frame
5378    */
5379   public List<? extends AlignmentViewPanel> getAlignPanels()
5380   {
5381     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5382   }
5383
5384   /**
5385    * Open a new alignment window, with the cDNA associated with this (protein)
5386    * alignment, aligned as is the protein.
5387    */
5388   protected void viewAsCdna_actionPerformed()
5389   {
5390     // TODO no longer a menu action - refactor as required
5391     final AlignmentI alignment = getViewport().getAlignment();
5392     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5393     if (mappings == null)
5394     {
5395       return;
5396     }
5397     List<SequenceI> cdnaSeqs = new ArrayList<>();
5398     for (SequenceI aaSeq : alignment.getSequences())
5399     {
5400       for (AlignedCodonFrame acf : mappings)
5401       {
5402         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5403         if (dnaSeq != null)
5404         {
5405           /*
5406            * There is a cDNA mapping for this protein sequence - add to new
5407            * alignment. It will share the same dataset sequence as other mapped
5408            * cDNA (no new mappings need to be created).
5409            */
5410           final Sequence newSeq = new Sequence(dnaSeq);
5411           newSeq.setDatasetSequence(dnaSeq);
5412           cdnaSeqs.add(newSeq);
5413         }
5414       }
5415     }
5416     if (cdnaSeqs.size() == 0)
5417     {
5418       // show a warning dialog no mapped cDNA
5419       return;
5420     }
5421     AlignmentI cdna = new Alignment(
5422             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5423     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5424             AlignFrame.DEFAULT_HEIGHT);
5425     cdna.alignAs(alignment);
5426     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5427             + this.title;
5428     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5429             AlignFrame.DEFAULT_HEIGHT);
5430   }
5431
5432   /**
5433    * Set visibility of dna/protein complement view (available when shown in a
5434    * split frame).
5435    *
5436    * @param show
5437    */
5438   @Override
5439   protected void showComplement_actionPerformed(boolean show)
5440   {
5441     SplitContainerI sf = getSplitViewContainer();
5442     if (sf != null)
5443     {
5444       sf.setComplementVisible(this, show);
5445     }
5446   }
5447
5448   /**
5449    * Generate the reverse (optionally complemented) of the selected sequences,
5450    * and add them to the alignment
5451    */
5452   @Override
5453   protected void showReverse_actionPerformed(boolean complement)
5454   {
5455     AlignmentI al = null;
5456     try
5457     {
5458       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5459       al = dna.reverseCdna(complement);
5460       viewport.addAlignment(al, "");
5461       addHistoryItem(new EditCommand(
5462               MessageManager.getString("label.add_sequences"), Action.PASTE,
5463               al.getSequencesArray(), 0, al.getWidth(),
5464               viewport.getAlignment()));
5465     } catch (Exception ex)
5466     {
5467       System.err.println(ex.getMessage());
5468       return;
5469     }
5470   }
5471
5472   /**
5473    * Try to run a script in the Groovy console, having first ensured that this
5474    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5475    * be targeted at this alignment.
5476    */
5477   @Override
5478   protected void runGroovy_actionPerformed()
5479   {
5480     Jalview.setCurrentAlignFrame(this);
5481     groovy.ui.Console console = Desktop.getGroovyConsole();
5482     if (console != null)
5483     {
5484       try
5485       {
5486         console.runScript();
5487       } catch (Exception ex)
5488       {
5489         System.err.println((ex.toString()));
5490         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5491                 MessageManager.getString("label.couldnt_run_groovy_script"),
5492                 MessageManager.getString("label.groovy_support_failed"),
5493                 JvOptionPane.ERROR_MESSAGE);
5494       }
5495     }
5496     else
5497     {
5498       System.err.println("Can't run Groovy script as console not found");
5499     }
5500   }
5501
5502   /**
5503    * Hides columns containing (or not containing) a specified feature, provided
5504    * that would not leave all columns hidden
5505    *
5506    * @param featureType
5507    * @param columnsContaining
5508    * @return
5509    */
5510   public boolean hideFeatureColumns(String featureType,
5511           boolean columnsContaining)
5512   {
5513     boolean notForHiding = avc.markColumnsContainingFeatures(
5514             columnsContaining, false, false, featureType);
5515     if (notForHiding)
5516     {
5517       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5518               false, featureType))
5519       {
5520         getViewport().hideSelectedColumns();
5521         return true;
5522       }
5523     }
5524     return false;
5525   }
5526
5527   @Override
5528   protected void selectHighlightedColumns_actionPerformed(
5529           ActionEvent actionEvent)
5530   {
5531     // include key modifier check in case user selects from menu
5532     avc.markHighlightedColumns(
5533             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5534             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5535                     | ActionEvent.CTRL_MASK)) != 0);
5536   }
5537
5538   /**
5539    * Rebuilds the Colour menu, including any user-defined colours which have
5540    * been loaded either on startup or during the session
5541    */
5542   public void buildColourMenu()
5543   {
5544     colourMenu.removeAll();
5545
5546     colourMenu.add(applyToAllGroups);
5547     colourMenu.add(textColour);
5548     colourMenu.addSeparator();
5549
5550     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5551             false);
5552
5553     colourMenu.addSeparator();
5554     colourMenu.add(conservationMenuItem);
5555     colourMenu.add(modifyConservation);
5556     colourMenu.add(abovePIDThreshold);
5557     colourMenu.add(modifyPID);
5558     colourMenu.add(annotationColour);
5559
5560     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5561     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5562   }
5563
5564   /**
5565    * Open a dialog (if not already open) that allows the user to select and
5566    * calculate PCA or Tree analysis
5567    */
5568   protected void openTreePcaDialog()
5569   {
5570     if (alignPanel.getCalculationDialog() == null)
5571     {
5572       new CalculationChooser(AlignFrame.this);
5573     }
5574   }
5575
5576   @Override
5577   protected void loadVcf_actionPerformed()
5578   {
5579     JalviewFileChooser chooser = new JalviewFileChooser(
5580             Cache.getProperty("LAST_DIRECTORY"));
5581     chooser.setFileView(new JalviewFileView());
5582     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5583     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5584
5585     int value = chooser.showOpenDialog(null);
5586
5587     if (value == JalviewFileChooser.APPROVE_OPTION)
5588     {
5589       String choice = chooser.getSelectedFile().getPath();
5590       Cache.setProperty("LAST_DIRECTORY", choice);
5591       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5592       new VCFLoader(choice).loadVCF(seqs, this);
5593     }
5594
5595   }
5596 }
5597
5598 class PrintThread extends Thread
5599 {
5600   AlignmentPanel ap;
5601
5602   public PrintThread(AlignmentPanel ap)
5603   {
5604     this.ap = ap;
5605   }
5606
5607   static PageFormat pf;
5608
5609   @Override
5610   public void run()
5611   {
5612     PrinterJob printJob = PrinterJob.getPrinterJob();
5613
5614     if (pf != null)
5615     {
5616       printJob.setPrintable(ap, pf);
5617     }
5618     else
5619     {
5620       printJob.setPrintable(ap);
5621     }
5622
5623     if (printJob.printDialog())
5624     {
5625       try
5626       {
5627         printJob.print();
5628       } catch (Exception PrintException)
5629       {
5630         PrintException.printStackTrace();
5631       }
5632     }
5633   }
5634 }